# Copyright 2012 by Wibowo Arindrarto.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Tests for SearchIO HmmerIO parsers."""


import os
import unittest

from Bio import BiopythonExperimentalWarning

import warnings


with warnings.catch_warnings():
    warnings.simplefilter('ignore', BiopythonExperimentalWarning)
    from Bio.SearchIO import parse

# test case files are in the Blast directory
TEST_DIR = 'Hmmer'
FMT = 'hmmer3-text'


def get_file(filename):
    """Returns the path of a test file."""
    return os.path.join(TEST_DIR, filename)


class HmmscanCases(unittest.TestCase):

    def test_31b1_hmmscan_001(self):
        "Test parsing hmmscan 3.1b1 (text_31b1_hmmscan_001)"

        txt_file = get_file('text_31b1_hmmscan_001.out')
        qresults = parse(txt_file, FMT)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmscan', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/protdb/Pfam-A.hmm', qresult.target)
        self.assertEqual('3.1b1', qresult.version)
        self.assertEqual('random_s00', qresult.id)
        self.assertEqual(22, qresult.seq_len)
        self.assertEqual(0, len(qresult))

        # test fifth result
        for qresult in qresults:
            counter += 1

        self.assertEqual('hmmscan', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/protdb/Pfam-A.hmm', qresult.target)
        self.assertEqual('3.1b1', qresult.version)
        self.assertEqual('gi|125490392|ref|NP_038661.2|', qresult.id)
        self.assertEqual('POU domain, class 5, transcription factor 1 isoform 1 [Mus musculus]', qresult.description)
        self.assertEqual(352, qresult.seq_len)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual('Pou', hit.id)
        self.assertEqual('Pou domain - N-terminal to homeobox domain', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(7.6e-37, hit.evalue)
        self.assertEqual(124.8, hit.bitscore)
        self.assertEqual(0.5, hit.bias)
        self.assertEqual(1.5, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(123.9, hsp.bitscore)
        self.assertEqual(0.5, hsp.bias)
        self.assertEqual(5e-40, hsp.evalue_cond)
        self.assertEqual(1.5e-36, hsp.evalue)
        self.assertEqual(2, hsp.hit_start)
        self.assertEqual(75, hsp.hit_end)
        self.assertEqual('.]', hsp.hit_endtype)
        self.assertEqual(132, hsp.query_start)
        self.assertEqual(205, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(130, hsp.env_start)
        self.assertEqual(205, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.97, hsp.acc_avg)
        self.assertEqual('eldleeleefakefkqrrikLgltqadvgsalgalyGkefsqttIcrFEalqLslknmckLkpllekWLeeae',
                str(hsp.hit.seq))
        self.assertEqual('KALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSLKNMCKLRPLLEKWVEEAD',
                str(hsp.query.seq))
        self.assertEqual('67899******************************************************************96',
                hsp.aln_annotation['PP'])

        # last hit
        hit = qresult[4]
        self.assertEqual('DUF521', hit.id)
        self.assertEqual('Protein of unknown function (DUF521)', hit.description)
        self.assertFalse(hit.is_included)
        self.assertEqual(0.15, hit.evalue)
        self.assertEqual(10.5, hit.bitscore)
        self.assertEqual(0.1, hit.bias)
        self.assertEqual(1.4, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(9.6, hsp.bitscore)
        self.assertEqual(0.1, hsp.bias)
        self.assertEqual(9.4e-05, hsp.evalue_cond)
        self.assertEqual(0.28, hsp.evalue)
        self.assertEqual(272, hsp.hit_start)
        self.assertEqual(334, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(220, hsp.query_start)
        self.assertEqual(280, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(196, hsp.env_start)
        self.assertEqual(294, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.77, hsp.acc_avg)
        self.assertEqual('adlaavleelnkakkeevdlvvlGcPhlsleeleelaellkgrkkkvsvelvvttsravlsk',
                str(hsp.hit.seq))
        self.assertEqual('QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEK--DVVRVWFCNRRQKGKR',
                str(hsp.query.seq))
        self.assertEqual('345666667778888899************************99..9999999988876554',
                hsp.aln_annotation['PP'])

        # test if we've properly finished iteration
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(5, counter)

    def test_30_hmmscan_001(self):
        "Test parsing hmmscan 3.0 (text_30_hmmscan_001)"

        txt_file = get_file('text_30_hmmscan_001.out')
        qresults = parse(txt_file, FMT)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmscan', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/Pfam-A.hmm', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('random_s00', qresult.id)
        self.assertEqual(32, qresult.seq_len)
        self.assertEqual(0, len(qresult))

        # test second result
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmscan', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/Pfam-A.hmm', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('gi|4885477|ref|NP_005359.1|', qresult.id)
        self.assertEqual('myoglobin [Homo sapiens]', qresult.description)
        self.assertEqual(154, qresult.seq_len)
        self.assertEqual(1, len(qresult))

        hit = qresult[0]
        self.assertEqual('Globin', hit.id)
        self.assertEqual('Globin', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(6e-21, hit.evalue)
        self.assertEqual(74.6, hit.bitscore)
        self.assertEqual(0.3, hit.bias)
        self.assertEqual(1.3, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(74.0, hsp.bitscore)
        self.assertEqual(0.2, hsp.bias)
        self.assertEqual(6.7e-25, hsp.evalue_cond)
        self.assertEqual(9.2e-21, hsp.evalue)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(107, hsp.hit_end)
        self.assertEqual('[.', hsp.hit_endtype)
        self.assertEqual(6, hsp.query_start)
        self.assertEqual(112, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(6, hsp.env_start)
        self.assertEqual(113, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.97, hsp.acc_avg)
        self.assertEqual('HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHSGGGGGGGCCCTTTT.HHHHHTSCHHHHHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHHHHTT-.--HHHHCCHHHHH',
                hsp.aln_annotation['CS'])
        self.assertEqual('qkalvkaswekvkanaeeigaeilkrlfkaypdtkklFkkfgdls.aedlksspkfkahakkvlaaldeavknldnddnlkaalkklgarHakrg.vdpanfklfgeal',
                str(hsp.hit.seq))
        self.assertEqual('EWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKsEDEMKASEDLKKHGATVLTALGGILKK---KGHHEAEIKPLAQSHATKHkIPVKYLEFISECI',
                str(hsp.query.seq))
        self.assertEqual('5789*********************************************************************...6899***********************999998',
                hsp.aln_annotation['PP'])

        # test third result
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmscan', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/Pfam-A.hmm', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('gi|126362951:116-221', qresult.id)
        self.assertEqual('leukocyte immunoglobulin-like receptor subfamily B member 1 isoform 2 precursor [Homo sapiens]', qresult.description)
        self.assertEqual(106, qresult.seq_len)
        self.assertEqual(2, len(qresult))

        hit = qresult[0]
        self.assertEqual('Ig_3', hit.id)
        self.assertEqual('Immunoglobulin domain', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(1.4e-09, hit.evalue)
        self.assertEqual(38.2, hit.bitscore)
        self.assertEqual(0.4, hit.bias)
        self.assertEqual(1.3, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(37.6, hsp.bitscore)
        self.assertEqual(0.3, hsp.bias)
        self.assertEqual(3e-13, hsp.evalue_cond)
        self.assertEqual(2.1e-09, hsp.evalue)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(73, hsp.hit_end)
        self.assertEqual('[.', hsp.hit_endtype)
        self.assertEqual(8, hsp.query_start)
        self.assertEqual(84, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(8, hsp.env_start)
        self.assertEqual(88, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.94, hsp.acc_avg)
        self.assertEqual('kPvisvspsptvtsggnvtLtCsaeggpppptisWy.....ietppelqgsegssssestLtissvtsedsgtYtCva',
                str(hsp.hit.seq))
        self.assertEqual('KPTLSAQPSPVVNSGGNVILQCDSQVA--FDGFSLCkegedEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYA',
                str(hsp.query.seq))
        self.assertEqual('8************************99..78888888****************************************9',
                hsp.aln_annotation['PP'])

        hit = qresult[-1]
        self.assertEqual('Ig_2', hit.id)
        self.assertEqual('Immunoglobulin domain', hit.description)
        self.assertEqual(3.5e-05, hit.evalue)
        self.assertEqual(23.7, hit.bitscore)
        self.assertEqual(0.1, hit.bias)
        self.assertEqual(1.1, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(23.4, hsp.bitscore)
        self.assertEqual(0.1, hsp.bias)
        self.assertEqual(6.2e-09, hsp.evalue_cond)
        self.assertEqual(4.3e-05, hsp.evalue)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(80, hsp.hit_end)
        self.assertEqual('[]', hsp.hit_endtype)
        self.assertEqual(8, hsp.query_start)
        self.assertEqual(104, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(8, hsp.env_start)
        self.assertEqual(104, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.71, hsp.acc_avg)
        self.assertEqual('kpvlvapp.svvtegenvtLtCsapgnptprvqwykdg.vels......qsqnq........lfipnvsaedsgtYtCra....rnseggktstsveltv',
                str(hsp.hit.seq))
        self.assertEqual('KPTLSAQPsPVVNSGGNVILQCDSQVA-FDGFSLCKEGeDEHPqclnsqP---HargssraiFSVGPVSPSRRWWYRCYAydsnSPYEWSLPSDLLELLV',
                str(hsp.query.seq))
        self.assertEqual('799998885779*************85.899***9988655554443320...134455543444669************88443344588888888766',
                hsp.aln_annotation['PP'])

        # test fourth result
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmscan', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/Pfam-A.hmm', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('gi|22748937|ref|NP_065801.1|', qresult.id)
        self.assertEqual('exportin-5 [Homo sapiens]', qresult.description)
        self.assertEqual(1204, qresult.seq_len)
        self.assertEqual(2, len(qresult))

        hit = qresult[0]
        self.assertEqual('Xpo1', hit.id)
        self.assertEqual('Exportin 1-like protein', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(7.8e-34, hit.evalue)
        self.assertEqual(116.6, hit.bitscore)
        self.assertEqual(7.8, hit.bias)
        self.assertEqual(2.8, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(116.1, hsp.bitscore)
        self.assertEqual(3.4, hsp.bias)
        self.assertEqual(1.6e-37, hsp.evalue_cond)
        self.assertEqual(1.1e-33, hsp.evalue)
        self.assertEqual(1, hsp.hit_start)
        self.assertEqual(148, hsp.hit_end)
        self.assertEqual('.]', hsp.hit_endtype)
        self.assertEqual(109, hsp.query_start)
        self.assertEqual(271, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(108, hsp.env_start)
        self.assertEqual(271, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.98, hsp.acc_avg)
        self.assertEqual('HHHHHHHHHHHHHHHHHHTTTTSTTHHHHHHHHHHG-HHHHHHHHHHHHHHHHHHCCS-TTTS-CCCHHHHHHHCHHHHHHHHHHHHHHHC-TT-..................HHHHHHHHHHHHHHCTTS-CHHCHCS...HHHHHCHHCCSCCCHHHHHHHH',
                hsp.aln_annotation['CS'])
        self.assertEqual('kflrnklaealaelflqeypnqWpsffddllsllssspsglelllriLkvlpeEiadfsrskleqerrnelkdllrsqvqkilelllqileqsvskk...............sselveatLkclsswvswidiglivnsp..llsllfqlLndpelreaAvecL',
                str(hsp.hit.seq))
        self.assertEqual('NHIKDALSRIVVEMIKREWPQHWPDMLIELDTLSKQGETQTELVMFILLRLAEDVVTF--QTLPPQRRRDIQQTLTQNMERIFSFLLNTLQENVNKYqqvktdtsqeskaqaNCRVGVAALNTLAGYIDWVSMSHITAENckLLEILCLLLNEQELQLGAAECL',
                str(hsp.query.seq))
        self.assertEqual('89******************************************************99..79*********************************99*****************************************8889*********************8',
                hsp.aln_annotation['PP'])

        hsp = hit.hsps[-1]
        self.assertEqual(2, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(-1.8, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(0.35, hsp.evalue_cond)
        self.assertEqual(2.4e+03, hsp.evalue)
        self.assertEqual(111, hsp.hit_start)
        self.assertEqual(139, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(498, hsp.query_start)
        self.assertEqual(525, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(495, hsp.env_start)
        self.assertEqual(529, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.86, hsp.acc_avg)
        self.assertEqual('HHCTTS-CHHCHCS.HHHHHCHHCCSCC',
                hsp.aln_annotation['CS'])
        self.assertEqual('swvswidiglivnspllsllfqlLndpe',
                str(hsp.hit.seq))
        self.assertEqual('SFVQWEAMTLFLES-VITQMFRTLNREE',
                str(hsp.query.seq))
        self.assertEqual('899*********98.8888899998776',
                hsp.aln_annotation['PP'])

        hit = qresult[-1]
        self.assertEqual('IBN_N', hit.id)
        self.assertEqual('Importin-beta N-terminal domain', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(0.0039, hit.evalue)
        self.assertEqual(16.9, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.7, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(14.0, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(4.8e-06, hsp.evalue_cond)
        self.assertEqual(0.033, hsp.evalue)
        self.assertEqual(3, hsp.hit_start)
        self.assertEqual(75, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(35, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(32, hsp.env_start)
        self.assertEqual(100, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.87, hsp.acc_avg)
        self.assertEqual('HHHHHHHSCTHHHHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHSCCHHHHHHHHCS-HHHHHHHHHHHHHHH',
                hsp.aln_annotation['CS'])
        self.assertEqual('qLnqlekqkPgflsallqilanksldlevRqlAalyLknlItkhWkseeaqrqqqlpeeekelIrnnllnll',
                str(hsp.hit.seq))
        self.assertEqual('FCEEFKEKCPICVPCGLRLA-EKTQVAIVRHFGLQILEHVVKFRWN--------GMSRLEKVYLKNSVMELI',
                str(hsp.query.seq))
        self.assertEqual('56788886699*********.6555899******************........999999****99999887',
                hsp.aln_annotation['PP'])

        hsp = hit.hsps[-1]
        self.assertEqual(2, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(-3.3, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(1.2, hsp.evalue_cond)
        self.assertEqual(8e+03, hsp.evalue)
        self.assertEqual(56, hsp.hit_start)
        self.assertEqual(75, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(167, hsp.query_start)
        self.assertEqual(186, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(164, hsp.env_start)
        self.assertEqual(187, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.85, hsp.acc_avg)
        self.assertEqual('HCS-HHHHHHHHHHHHHHH',
                hsp.aln_annotation['CS'])
        self.assertEqual('qqlpeeekelIrnnllnll',
                str(hsp.hit.seq))
        self.assertEqual('QTLPPQRRRDIQQTLTQNM',
                str(hsp.query.seq))
        self.assertEqual('6899*******99998865',
                hsp.aln_annotation['PP'])

        # test fifth result
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmscan', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/Pfam-A.hmm', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('gi|125490392|ref|NP_038661.2|', qresult.id)
        self.assertEqual('POU domain, class 5, transcription factor 1 isoform 1 [Mus musculus]', qresult.description)
        self.assertEqual(352, qresult.seq_len)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual('Pou', hit.id)
        self.assertEqual('Pou domain - N-terminal to homeobox domain', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(7e-37, hit.evalue)
        self.assertEqual(124.8, hit.bitscore)
        self.assertEqual(0.5, hit.bias)
        self.assertEqual(1.5, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(123.9, hsp.bitscore)
        self.assertEqual(0.3, hsp.bias)
        self.assertEqual(5e-40, hsp.evalue_cond)
        self.assertEqual(1.4e-36, hsp.evalue)
        self.assertEqual(2, hsp.hit_start)
        self.assertEqual(75, hsp.hit_end)
        self.assertEqual('.]', hsp.hit_endtype)
        self.assertEqual(132, hsp.query_start)
        self.assertEqual(205, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(130, hsp.env_start)
        self.assertEqual(205, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.97, hsp.acc_avg)
        self.assertEqual('eldleeleefakefkqrrikLgltqadvgsalgalyGkefsqttIcrFEalqLslknmckLkpllekWLeeae',
                str(hsp.hit.seq))
        self.assertEqual('KALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSLKNMCKLRPLLEKWVEEAD',
                str(hsp.query.seq))
        self.assertEqual('67899******************************************************************96',
                hsp.aln_annotation['PP'])

        hit = qresult[1]
        self.assertEqual('Homeobox', hit.id)
        self.assertEqual('Homeobox domain', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(2.1e-18, hit.evalue)
        self.assertEqual(65.5, hit.bitscore)
        self.assertEqual(1.1, hit.bias)
        self.assertEqual(1.5, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(64.6, hsp.bitscore)
        self.assertEqual(0.7, hsp.bias)
        self.assertEqual(1.5e-21, hsp.evalue_cond)
        self.assertEqual(4.1e-18, hsp.evalue)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(57, hsp.hit_end)
        self.assertEqual('[]', hsp.hit_endtype)
        self.assertEqual(223, hsp.query_start)
        self.assertEqual(280, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(223, hsp.env_start)
        self.assertEqual(280, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.98, hsp.acc_avg)
        self.assertEqual('SS--SS--HHHHHHHHHHCCTSSS--HHHHHHHHHH----HHHHHHHHHHHHHHHHH',
                hsp.aln_annotation['CS'])
        self.assertEqual('rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk',
                str(hsp.hit.seq))
        self.assertEqual('KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR',
                str(hsp.query.seq))
        self.assertEqual('79****************************************************997',
                hsp.aln_annotation['PP'])

        hit = qresult[2]
        self.assertEqual('HTH_31', hit.id)
        self.assertEqual('Helix-turn-helix domain', hit.description)
        self.assertFalse(hit.is_included)
        self.assertEqual(0.012, hit.evalue)
        self.assertEqual(15.6, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.2, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(12.0, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(5.7e-05, hsp.evalue_cond)
        self.assertEqual(0.16, hsp.evalue)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(35, hsp.hit_end)
        self.assertEqual('[.', hsp.hit_endtype)
        self.assertEqual(140, hsp.query_start)
        self.assertEqual(181, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(140, hsp.env_start)
        self.assertEqual(184, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.96, hsp.acc_avg)
        self.assertEqual('aLGarLralReraGLtqeevAerlg......vSastlsrlE',
                str(hsp.hit.seq))
        self.assertEqual('QFAKLLKQKRITLGYTQADVGLTLGvlfgkvFSQTTICRFE',
                str(hsp.query.seq))
        self.assertEqual('6999***********************************99',
                hsp.aln_annotation['PP'])

        hsp = hit.hsps[1]
        self.assertEqual(2, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(0.8, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(0.19, hsp.evalue_cond)
        self.assertEqual(5.2e+02, hsp.evalue)
        self.assertEqual(38, hsp.hit_start)
        self.assertEqual(62, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(244, hsp.query_start)
        self.assertEqual(268, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(242, hsp.env_start)
        self.assertEqual(270, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.86, hsp.acc_avg)
        self.assertEqual('rgrpsaavlaalaralgldpaera',
                str(hsp.hit.seq))
        self.assertEqual('CPKPSLQQITHIANQLGLEKDVVR',
                str(hsp.query.seq))
        self.assertEqual('678**************9988765',
                hsp.aln_annotation['PP'])

        hit = qresult[3]
        self.assertEqual('Homeobox_KN', hit.id)
        self.assertEqual('Homeobox KN domain', hit.description)
        self.assertFalse(hit.is_included)
        self.assertEqual(0.039, hit.evalue)
        self.assertEqual(13.5, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(1.6, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(12.3, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(3.5e-05, hsp.evalue_cond)
        self.assertEqual(0.095, hsp.evalue)
        self.assertEqual(6, hsp.hit_start)
        self.assertEqual(39, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(243, hsp.query_start)
        self.assertEqual(276, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(240, hsp.env_start)
        self.assertEqual(277, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.91, hsp.acc_avg)
        self.assertEqual('hnPYPskevkeelakqTglsrkqidnWFiNaRr',
                str(hsp.hit.seq))
        self.assertEqual('KCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQ',
                str(hsp.query.seq))
        self.assertEqual('56779*************************996',
                hsp.aln_annotation['PP'])

        hit = qresult[4]
        self.assertEqual('DUF521', hit.id)
        self.assertEqual('Protein of unknown function (DUF521)', hit.description)
        self.assertFalse(hit.is_included)
        self.assertEqual(0.14, hit.evalue)
        self.assertEqual(10.5, hit.bitscore)
        self.assertEqual(0.1, hit.bias)
        self.assertEqual(1.4, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(9.6, hsp.bitscore)
        self.assertEqual(0.1, hsp.bias)
        self.assertEqual(9.4e-05, hsp.evalue_cond)
        self.assertEqual(0.26, hsp.evalue)
        self.assertEqual(272, hsp.hit_start)
        self.assertEqual(334, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(220, hsp.query_start)
        self.assertEqual(280, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(196, hsp.env_start)
        self.assertEqual(294, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.77, hsp.acc_avg)
        self.assertEqual('adlaavleelnkakkeevdlvvlGcPhlsleeleelaellkgrkkkvsvelvvttsravlsk',
                str(hsp.hit.seq))
        self.assertEqual('QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEK--DVVRVWFCNRRQKGKR',
                str(hsp.query.seq))
        self.assertEqual('345666667778888899************************99..9999999988876554',
                hsp.aln_annotation['PP'])

        # test if we've properly finished iteration
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(5, counter)

    def test_30_hmmscan_002(self):
        "Test parsing hmmscan 3.0 (text_30_hmmscan_002)"

        txt_file = get_file('text_30_hmmscan_002.out')
        qresults = parse(txt_file, FMT)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmscan', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/Pfam-A.hmm', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('random_s00', qresult.id)
        self.assertEqual(32, qresult.seq_len)
        self.assertEqual(0, len(qresult))

        # test if we've properly finished iteration
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_30_hmmscan_003(self):
        "Test parsing hmmscan 3.0 (text_30_hmmscan_003)"

        txt_file = get_file('text_30_hmmscan_003.out')
        qresults = parse(txt_file, FMT)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmscan', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/Pfam-A.hmm', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('gi|4885477|ref|NP_005359.1|', qresult.id)
        self.assertEqual('myoglobin [Homo sapiens]', qresult.description)
        self.assertEqual(154, qresult.seq_len)
        self.assertEqual(1, len(qresult))

        hit = qresult[0]
        self.assertEqual('Globin', hit.id)
        self.assertEqual('Globin', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(6e-21, hit.evalue)
        self.assertEqual(74.6, hit.bitscore)
        self.assertEqual(0.3, hit.bias)
        self.assertEqual(1.3, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(74.0, hsp.bitscore)
        self.assertEqual(0.2, hsp.bias)
        self.assertEqual(6.7e-25, hsp.evalue_cond)
        self.assertEqual(9.2e-21, hsp.evalue)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(107, hsp.hit_end)
        self.assertEqual('[.', hsp.hit_endtype)
        self.assertEqual(6, hsp.query_start)
        self.assertEqual(112, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(6, hsp.env_start)
        self.assertEqual(113, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.97, hsp.acc_avg)
        self.assertEqual('HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHSGGGGGGGCCCTTTT.HHHHHTSCHHHHHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHHHHTT-.--HHHHCCHHHHH',
                hsp.aln_annotation['CS'])
        self.assertEqual('qkalvkaswekvkanaeeigaeilkrlfkaypdtkklFkkfgdls.aedlksspkfkahakkvlaaldeavknldnddnlkaalkklgarHakrg.vdpanfklfgeal',
                str(hsp.hit.seq))
        self.assertEqual('EWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKsEDEMKASEDLKKHGATVLTALGGILKK---KGHHEAEIKPLAQSHATKHkIPVKYLEFISECI',
                str(hsp.query.seq))
        self.assertEqual('5789*********************************************************************...6899***********************999998',
                hsp.aln_annotation['PP'])

        # test if we've properly finished iteration
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_30_hmmscan_004(self):
        "Test parsing hmmscan 3.0 (text_30_hmmscan_004)"

        txt_file = get_file('text_30_hmmscan_004.out')
        qresults = parse(txt_file, FMT)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmscan', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/Pfam-A.hmm', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('gi|126362951:116-221', qresult.id)
        self.assertEqual('leukocyte immunoglobulin-like receptor subfamily B member 1 isoform 2 precursor [Homo sapiens]', qresult.description)
        self.assertEqual(106, qresult.seq_len)
        self.assertEqual(2, len(qresult))

        hit = qresult[0]
        self.assertEqual('Ig_3', hit.id)
        self.assertEqual('Immunoglobulin domain', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(1.4e-09, hit.evalue)
        self.assertEqual(38.2, hit.bitscore)
        self.assertEqual(0.4, hit.bias)
        self.assertEqual(1.3, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(37.6, hsp.bitscore)
        self.assertEqual(0.3, hsp.bias)
        self.assertEqual(3e-13, hsp.evalue_cond)
        self.assertEqual(2.1e-09, hsp.evalue)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(73, hsp.hit_end)
        self.assertEqual('[.', hsp.hit_endtype)
        self.assertEqual(8, hsp.query_start)
        self.assertEqual(84, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(8, hsp.env_start)
        self.assertEqual(88, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.94, hsp.acc_avg)
        self.assertEqual('kPvisvspsptvtsggnvtLtCsaeggpppptisWy.....ietppelqgsegssssestLtissvtsedsgtYtCva',
                str(hsp.hit.seq))
        self.assertEqual('KPTLSAQPSPVVNSGGNVILQCDSQVA--FDGFSLCkegedEHPQCLNSQPHARGSSRAIFSVGPVSPSRRWWYRCYA',
                str(hsp.query.seq))
        self.assertEqual('8************************99..78888888****************************************9',
                hsp.aln_annotation['PP'])

        hit = qresult[-1]
        self.assertEqual('Ig_2', hit.id)
        self.assertEqual('Immunoglobulin domain', hit.description)
        self.assertEqual(3.5e-05, hit.evalue)
        self.assertEqual(23.7, hit.bitscore)
        self.assertEqual(0.1, hit.bias)
        self.assertEqual(1.1, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(23.4, hsp.bitscore)
        self.assertEqual(0.1, hsp.bias)
        self.assertEqual(6.2e-09, hsp.evalue_cond)
        self.assertEqual(4.3e-05, hsp.evalue)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(80, hsp.hit_end)
        self.assertEqual('[]', hsp.hit_endtype)
        self.assertEqual(8, hsp.query_start)
        self.assertEqual(104, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(8, hsp.env_start)
        self.assertEqual(104, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.71, hsp.acc_avg)
        self.assertEqual('kpvlvapp.svvtegenvtLtCsapgnptprvqwykdg.vels......qsqnq........lfipnvsaedsgtYtCra....rnseggktstsveltv',
                str(hsp.hit.seq))
        self.assertEqual('KPTLSAQPsPVVNSGGNVILQCDSQVA-FDGFSLCKEGeDEHPqclnsqP---HargssraiFSVGPVSPSRRWWYRCYAydsnSPYEWSLPSDLLELLV',
                str(hsp.query.seq))
        self.assertEqual('799998885779*************85.899***9988655554443320...134455543444669************88443344588888888766',
                hsp.aln_annotation['PP'])

        # test if we've properly finished iteration
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_30_hmmscan_005(self):
        "Test parsing hmmscan 3.0 (text_30_hmmscan_005)"

        txt_file = get_file('text_30_hmmscan_005.out')
        qresults = parse(txt_file, FMT)
        counter = 0

        # test first result
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmscan', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/Pfam-A.hmm', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('gi|22748937|ref|NP_065801.1|', qresult.id)
        self.assertEqual('exportin-5 [Homo sapiens]', qresult.description)
        self.assertEqual(1204, qresult.seq_len)
        self.assertEqual(2, len(qresult))

        hit = qresult[0]
        self.assertEqual('Xpo1', hit.id)
        self.assertEqual('Exportin 1-like protein', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(7.8e-34, hit.evalue)
        self.assertEqual(116.6, hit.bitscore)
        self.assertEqual(7.8, hit.bias)
        self.assertEqual(2.8, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(116.1, hsp.bitscore)
        self.assertEqual(3.4, hsp.bias)
        self.assertEqual(1.6e-37, hsp.evalue_cond)
        self.assertEqual(1.1e-33, hsp.evalue)
        self.assertEqual(1, hsp.hit_start)
        self.assertEqual(148, hsp.hit_end)
        self.assertEqual('.]', hsp.hit_endtype)
        self.assertEqual(109, hsp.query_start)
        self.assertEqual(271, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(108, hsp.env_start)
        self.assertEqual(271, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.98, hsp.acc_avg)
        self.assertEqual('HHHHHHHHHHHHHHHHHHTTTTSTTHHHHHHHHHHG-HHHHHHHHHHHHHHHHHHCCS-TTTS-CCCHHHHHHHCHHHHHHHHHHHHHHHC-TT-..................HHHHHHHHHHHHHHCTTS-CHHCHCS...HHHHHCHHCCSCCCHHHHHHHH',
                hsp.aln_annotation['CS'])
        self.assertEqual('kflrnklaealaelflqeypnqWpsffddllsllssspsglelllriLkvlpeEiadfsrskleqerrnelkdllrsqvqkilelllqileqsvskk...............sselveatLkclsswvswidiglivnsp..llsllfqlLndpelreaAvecL',
                str(hsp.hit.seq))
        self.assertEqual('NHIKDALSRIVVEMIKREWPQHWPDMLIELDTLSKQGETQTELVMFILLRLAEDVVTF--QTLPPQRRRDIQQTLTQNMERIFSFLLNTLQENVNKYqqvktdtsqeskaqaNCRVGVAALNTLAGYIDWVSMSHITAENckLLEILCLLLNEQELQLGAAECL',
                str(hsp.query.seq))
        self.assertEqual('89******************************************************99..79*********************************99*****************************************8889*********************8',
                hsp.aln_annotation['PP'])

        hsp = hit.hsps[-1]
        self.assertEqual(2, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(-1.8, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(0.35, hsp.evalue_cond)
        self.assertEqual(2.4e+03, hsp.evalue)
        self.assertEqual(111, hsp.hit_start)
        self.assertEqual(139, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(498, hsp.query_start)
        self.assertEqual(525, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(495, hsp.env_start)
        self.assertEqual(529, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.86, hsp.acc_avg)
        self.assertEqual('HHCTTS-CHHCHCS.HHHHHCHHCCSCC',
                hsp.aln_annotation['CS'])
        self.assertEqual('swvswidiglivnspllsllfqlLndpe',
                str(hsp.hit.seq))
        self.assertEqual('SFVQWEAMTLFLES-VITQMFRTLNREE',
                str(hsp.query.seq))
        self.assertEqual('899*********98.8888899998776',
                hsp.aln_annotation['PP'])

        hit = qresult[-1]
        self.assertEqual('IBN_N', hit.id)
        self.assertEqual('Importin-beta N-terminal domain', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(0.0039, hit.evalue)
        self.assertEqual(16.9, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.7, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(14.0, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(4.8e-06, hsp.evalue_cond)
        self.assertEqual(0.033, hsp.evalue)
        self.assertEqual(3, hsp.hit_start)
        self.assertEqual(75, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(35, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(32, hsp.env_start)
        self.assertEqual(100, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.87, hsp.acc_avg)
        self.assertEqual('HHHHHHHSCTHHHHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHSCCHHHHHHHHCS-HHHHHHHHHHHHHHH',
                hsp.aln_annotation['CS'])
        self.assertEqual('qLnqlekqkPgflsallqilanksldlevRqlAalyLknlItkhWkseeaqrqqqlpeeekelIrnnllnll',
                str(hsp.hit.seq))
        self.assertEqual('FCEEFKEKCPICVPCGLRLA-EKTQVAIVRHFGLQILEHVVKFRWN--------GMSRLEKVYLKNSVMELI',
                str(hsp.query.seq))
        self.assertEqual('56788886699*********.6555899******************........999999****99999887',
                hsp.aln_annotation['PP'])

        hsp = hit.hsps[-1]
        self.assertEqual(2, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(-3.3, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(1.2, hsp.evalue_cond)
        self.assertEqual(8e+03, hsp.evalue)
        self.assertEqual(56, hsp.hit_start)
        self.assertEqual(75, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(167, hsp.query_start)
        self.assertEqual(186, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(164, hsp.env_start)
        self.assertEqual(187, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.85, hsp.acc_avg)
        self.assertEqual('HCS-HHHHHHHHHHHHHHH',
                hsp.aln_annotation['CS'])
        self.assertEqual('qqlpeeekelIrnnllnll',
                str(hsp.hit.seq))
        self.assertEqual('QTLPPQRRRDIQQTLTQNM',
                str(hsp.query.seq))
        self.assertEqual('6899*******99998865',
                hsp.aln_annotation['PP'])

        # test if we've properly finished iteration
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_30_hmmscan_006(self):
        "Test parsing hmmscan 3.0 (text_30_hmmscan_006)"

        txt_file = get_file('text_30_hmmscan_006.out')
        qresults = parse(txt_file, FMT)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmscan', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/Pfam-A.hmm', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('gi|125490392|ref|NP_038661.2|', qresult.id)
        self.assertEqual('POU domain, class 5, transcription factor 1 isoform 1 [Mus musculus]', qresult.description)
        self.assertEqual(352, qresult.seq_len)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual('Pou', hit.id)
        self.assertEqual('Pou domain - N-terminal to homeobox domain', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(7e-37, hit.evalue)
        self.assertEqual(124.8, hit.bitscore)
        self.assertEqual(0.5, hit.bias)
        self.assertEqual(1.5, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(123.9, hsp.bitscore)
        self.assertEqual(0.3, hsp.bias)
        self.assertEqual(5e-40, hsp.evalue_cond)
        self.assertEqual(1.4e-36, hsp.evalue)
        self.assertEqual(2, hsp.hit_start)
        self.assertEqual(75, hsp.hit_end)
        self.assertEqual('.]', hsp.hit_endtype)
        self.assertEqual(132, hsp.query_start)
        self.assertEqual(205, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(130, hsp.env_start)
        self.assertEqual(205, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.97, hsp.acc_avg)
        self.assertEqual('eldleeleefakefkqrrikLgltqadvgsalgalyGkefsqttIcrFEalqLslknmckLkpllekWLeeae',
                str(hsp.hit.seq))
        self.assertEqual('KALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSLKNMCKLRPLLEKWVEEAD',
                str(hsp.query.seq))
        self.assertEqual('67899******************************************************************96',
                hsp.aln_annotation['PP'])

        hit = qresult[1]
        self.assertEqual('Homeobox', hit.id)
        self.assertEqual('Homeobox domain', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(2.1e-18, hit.evalue)
        self.assertEqual(65.5, hit.bitscore)
        self.assertEqual(1.1, hit.bias)
        self.assertEqual(1.5, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(64.6, hsp.bitscore)
        self.assertEqual(0.7, hsp.bias)
        self.assertEqual(1.5e-21, hsp.evalue_cond)
        self.assertEqual(4.1e-18, hsp.evalue)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(57, hsp.hit_end)
        self.assertEqual('[]', hsp.hit_endtype)
        self.assertEqual(223, hsp.query_start)
        self.assertEqual(280, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(223, hsp.env_start)
        self.assertEqual(280, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.98, hsp.acc_avg)
        self.assertEqual('SS--SS--HHHHHHHHHHCCTSSS--HHHHHHHHHH----HHHHHHHHHHHHHHHHH',
                hsp.aln_annotation['CS'])
        self.assertEqual('rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk',
                str(hsp.hit.seq))
        self.assertEqual('KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR',
                str(hsp.query.seq))
        self.assertEqual('79****************************************************997',
                hsp.aln_annotation['PP'])

        hit = qresult[2]
        self.assertEqual('HTH_31', hit.id)
        self.assertEqual('Helix-turn-helix domain', hit.description)
        self.assertFalse(hit.is_included)
        self.assertEqual(0.012, hit.evalue)
        self.assertEqual(15.6, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.2, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(12.0, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(5.7e-05, hsp.evalue_cond)
        self.assertEqual(0.16, hsp.evalue)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(35, hsp.hit_end)
        self.assertEqual('[.', hsp.hit_endtype)
        self.assertEqual(140, hsp.query_start)
        self.assertEqual(181, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(140, hsp.env_start)
        self.assertEqual(184, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.96, hsp.acc_avg)
        self.assertEqual('aLGarLralReraGLtqeevAerlg......vSastlsrlE',
                str(hsp.hit.seq))
        self.assertEqual('QFAKLLKQKRITLGYTQADVGLTLGvlfgkvFSQTTICRFE',
                str(hsp.query.seq))
        self.assertEqual('6999***********************************99',
                hsp.aln_annotation['PP'])

        hsp = hit.hsps[1]
        self.assertEqual(2, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(0.8, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(0.19, hsp.evalue_cond)
        self.assertEqual(5.2e+02, hsp.evalue)
        self.assertEqual(38, hsp.hit_start)
        self.assertEqual(62, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(244, hsp.query_start)
        self.assertEqual(268, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(242, hsp.env_start)
        self.assertEqual(270, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.86, hsp.acc_avg)
        self.assertEqual('rgrpsaavlaalaralgldpaera',
                str(hsp.hit.seq))
        self.assertEqual('CPKPSLQQITHIANQLGLEKDVVR',
                str(hsp.query.seq))
        self.assertEqual('678**************9988765',
                hsp.aln_annotation['PP'])

        hit = qresult[3]
        self.assertEqual('Homeobox_KN', hit.id)
        self.assertEqual('Homeobox KN domain', hit.description)
        self.assertFalse(hit.is_included)
        self.assertEqual(0.039, hit.evalue)
        self.assertEqual(13.5, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(1.6, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(12.3, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(3.5e-05, hsp.evalue_cond)
        self.assertEqual(0.095, hsp.evalue)
        self.assertEqual(6, hsp.hit_start)
        self.assertEqual(39, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(243, hsp.query_start)
        self.assertEqual(276, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(240, hsp.env_start)
        self.assertEqual(277, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.91, hsp.acc_avg)
        self.assertEqual('hnPYPskevkeelakqTglsrkqidnWFiNaRr',
                str(hsp.hit.seq))
        self.assertEqual('KCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQ',
                str(hsp.query.seq))
        self.assertEqual('56779*************************996',
                hsp.aln_annotation['PP'])

        hit = qresult[4]
        self.assertEqual('DUF521', hit.id)
        self.assertEqual('Protein of unknown function (DUF521)', hit.description)
        self.assertFalse(hit.is_included)
        self.assertEqual(0.14, hit.evalue)
        self.assertEqual(10.5, hit.bitscore)
        self.assertEqual(0.1, hit.bias)
        self.assertEqual(1.4, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(9.6, hsp.bitscore)
        self.assertEqual(0.1, hsp.bias)
        self.assertEqual(9.4e-05, hsp.evalue_cond)
        self.assertEqual(0.26, hsp.evalue)
        self.assertEqual(272, hsp.hit_start)
        self.assertEqual(334, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(220, hsp.query_start)
        self.assertEqual(280, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(196, hsp.env_start)
        self.assertEqual(294, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.77, hsp.acc_avg)
        self.assertEqual('adlaavleelnkakkeevdlvvlGcPhlsleeleelaellkgrkkkvsvelvvttsravlsk',
                str(hsp.hit.seq))
        self.assertEqual('QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEK--DVVRVWFCNRRQKGKR',
                str(hsp.query.seq))
        self.assertEqual('345666667778888899************************99..9999999988876554',
                hsp.aln_annotation['PP'])

        # test if we've properly finished iteration
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_30_hmmscan_007(self):
        "Test parsing hmmscan 3.0 (text_30_hmmscan_007)"

        txt_file = get_file('text_30_hmmscan_007.out')
        qresults = parse(txt_file, FMT)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmscan', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/Pfam-A.hmm', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('gi|125490392|ref|NP_038661.2|', qresult.id)
        self.assertEqual('POU domain, class 5, transcription factor 1 isoform 1 [Mus musculus]', qresult.description)
        self.assertEqual(352, qresult.seq_len)
        self.assertEqual(5, len(qresult))

        hit = qresult[0]
        self.assertEqual('Pou', hit.id)
        self.assertEqual('Pou domain - N-terminal to homeobox domain', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(7e-37, hit.evalue)
        self.assertEqual(124.8, hit.bitscore)
        self.assertEqual(0.5, hit.bias)
        self.assertEqual(1.5, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(123.9, hsp.bitscore)
        self.assertEqual(0.3, hsp.bias)
        self.assertEqual(5e-40, hsp.evalue_cond)
        self.assertEqual(1.4e-36, hsp.evalue)
        self.assertEqual(2, hsp.hit_start)
        self.assertEqual(75, hsp.hit_end)
        self.assertEqual('.]', hsp.hit_endtype)
        self.assertEqual(132, hsp.query_start)
        self.assertEqual(205, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(130, hsp.env_start)
        self.assertEqual(205, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.97, hsp.acc_avg)

        hit = qresult[1]
        self.assertEqual('Homeobox', hit.id)
        self.assertEqual('Homeobox domain', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(2.1e-18, hit.evalue)
        self.assertEqual(65.5, hit.bitscore)
        self.assertEqual(1.1, hit.bias)
        self.assertEqual(1.5, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(64.6, hsp.bitscore)
        self.assertEqual(0.7, hsp.bias)
        self.assertEqual(1.5e-21, hsp.evalue_cond)
        self.assertEqual(4.1e-18, hsp.evalue)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(57, hsp.hit_end)
        self.assertEqual('[]', hsp.hit_endtype)
        self.assertEqual(223, hsp.query_start)
        self.assertEqual(280, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(223, hsp.env_start)
        self.assertEqual(280, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.98, hsp.acc_avg)

        hit = qresult[2]
        self.assertEqual('HTH_31', hit.id)
        self.assertEqual('Helix-turn-helix domain', hit.description)
        self.assertFalse(hit.is_included)
        self.assertEqual(0.012, hit.evalue)
        self.assertEqual(15.6, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.2, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(12.0, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(5.7e-05, hsp.evalue_cond)
        self.assertEqual(0.16, hsp.evalue)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(35, hsp.hit_end)
        self.assertEqual('[.', hsp.hit_endtype)
        self.assertEqual(140, hsp.query_start)
        self.assertEqual(181, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(140, hsp.env_start)
        self.assertEqual(184, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.96, hsp.acc_avg)

        hsp = hit.hsps[1]
        self.assertEqual(2, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(0.8, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(0.19, hsp.evalue_cond)
        self.assertEqual(5.2e+02, hsp.evalue)
        self.assertEqual(38, hsp.hit_start)
        self.assertEqual(62, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(244, hsp.query_start)
        self.assertEqual(268, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(242, hsp.env_start)
        self.assertEqual(270, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.86, hsp.acc_avg)

        hit = qresult[3]
        self.assertEqual('Homeobox_KN', hit.id)
        self.assertEqual('Homeobox KN domain', hit.description)
        self.assertFalse(hit.is_included)
        self.assertEqual(0.039, hit.evalue)
        self.assertEqual(13.5, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(1.6, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(12.3, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(3.5e-05, hsp.evalue_cond)
        self.assertEqual(0.095, hsp.evalue)
        self.assertEqual(6, hsp.hit_start)
        self.assertEqual(39, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(243, hsp.query_start)
        self.assertEqual(276, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(240, hsp.env_start)
        self.assertEqual(277, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.91, hsp.acc_avg)

        hit = qresult[4]
        self.assertEqual('DUF521', hit.id)
        self.assertEqual('Protein of unknown function (DUF521)', hit.description)
        self.assertFalse(hit.is_included)
        self.assertEqual(0.14, hit.evalue)
        self.assertEqual(10.5, hit.bitscore)
        self.assertEqual(0.1, hit.bias)
        self.assertEqual(1.4, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(9.6, hsp.bitscore)
        self.assertEqual(0.1, hsp.bias)
        self.assertEqual(9.4e-05, hsp.evalue_cond)
        self.assertEqual(0.26, hsp.evalue)
        self.assertEqual(272, hsp.hit_start)
        self.assertEqual(334, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(220, hsp.query_start)
        self.assertEqual(280, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(196, hsp.env_start)
        self.assertEqual(294, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.77, hsp.acc_avg)

        # test if we've properly finished iteration
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_30_hmmscan_008(self):
        "Test parsing hmmscan 3.0 (text_30_hmmscan_008)"

        txt_file = get_file('text_30_hmmscan_008.out')
        qresults = parse(txt_file, FMT)
        counter = 0

        # test first result
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmscan', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/Pfam-A.hmm', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('gi|22748937|ref|NP_065801.1|', qresult.id)
        self.assertEqual('exportin-5 [Homo sapiens]', qresult.description)
        self.assertEqual(1204, qresult.seq_len)
        self.assertEqual(2, len(qresult))

        hit = qresult[0]
        self.assertEqual('Xpo1', hit.id)
        self.assertEqual('Exportin 1-like protein', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(7.8e-34, hit.evalue)
        self.assertEqual(116.6, hit.bitscore)
        self.assertEqual(7.8, hit.bias)
        self.assertEqual(2.8, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(116.1, hsp.bitscore)
        self.assertEqual(3.4, hsp.bias)
        self.assertEqual(1.6e-37, hsp.evalue_cond)
        self.assertEqual(1.1e-33, hsp.evalue)
        self.assertEqual(1, hsp.hit_start)
        self.assertEqual(148, hsp.hit_end)
        self.assertEqual('.]', hsp.hit_endtype)
        self.assertEqual(109, hsp.query_start)
        self.assertEqual(271, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(108, hsp.env_start)
        self.assertEqual(271, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.98, hsp.acc_avg)
        self.assertEqual('HHHHHHHHHHHHHHHHHHTTTTSTTHHHHHHHHHHG-HHHHHHHHHHHHHHHHHHCCS-TTTS-CCCHHHHHHHCHHHHHHHHHHHHHHHC-TT-..................HHHHHHHHHHHHHHCTTS-CHHCHCS...HHHHHCHHCCSCCCHHHHHHHH',
                hsp.aln_annotation['CS'])
        self.assertEqual('kflrnklaealaelflqeypnqWpsffddllsllssspsglelllriLkvlpeEiadfsrskleqerrnelkdllrsqvqkilelllqileqsvskk...............sselveatLkclsswvswidiglivnsp..llsllfqlLndpelreaAvecL',
                str(hsp.hit.seq))
        self.assertEqual('NHIKDALSRIVVEMIKREWPQHWPDMLIELDTLSKQGETQTELVMFILLRLAEDVVTF--QTLPPQRRRDIQQTLTQNMERIFSFLLNTLQENVNKYqqvktdtsqeskaqaNCRVGVAALNTLAGYIDWVSMSHITAENckLLEILCLLLNEQELQLGAAECL',
                str(hsp.query.seq))
        self.assertEqual('89******************************************************99..79*********************************99*****************************************8889*********************8',
                hsp.aln_annotation['PP'])

        hsp = hit.hsps[-1]
        self.assertEqual(2, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(-1.8, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(0.35, hsp.evalue_cond)
        self.assertEqual(2.4e+03, hsp.evalue)
        self.assertEqual(111, hsp.hit_start)
        self.assertEqual(139, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(498, hsp.query_start)
        self.assertEqual(525, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(495, hsp.env_start)
        self.assertEqual(529, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.86, hsp.acc_avg)
        self.assertEqual('HHCTTS-CHHCHCS.HHHHHCHHCCSCC',
                hsp.aln_annotation['CS'])
        self.assertEqual('swvswidiglivnspllsllfqlLndpe',
                str(hsp.hit.seq))
        self.assertEqual('SFVQWEAMTLFLES-VITQMFRTLNREE',
                str(hsp.query.seq))
        self.assertEqual('899*********98.8888899998776',
                hsp.aln_annotation['PP'])

        hit = qresult[-1]
        self.assertEqual('IBN_N', hit.id)
        self.assertEqual('Importin-beta N-terminal domain', hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(0.0039, hit.evalue)
        self.assertEqual(16.9, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.7, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(14.0, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(4.8e-06, hsp.evalue_cond)
        self.assertEqual(0.033, hsp.evalue)
        self.assertEqual(3, hsp.hit_start)
        self.assertEqual(75, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(35, hsp.query_start)
        self.assertEqual(98, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(32, hsp.env_start)
        self.assertEqual(100, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.87, hsp.acc_avg)
        self.assertEqual('HHHHHHHSCTHHHHHHHHHHHTTTSTHHHHHHHHHHHHHHHHHSCCHHHHHHHHCS-HHHHHHHHHHHHHHH',
                hsp.aln_annotation['CS'])
        self.assertEqual('qLnqlekqkPgflsallqilanksldlevRqlAalyLknlItkhWkseeaqrqqqlpeeekelIrnnllnll',
                str(hsp.hit.seq))
        self.assertEqual('FCEEFKEKCPICVPCGLRLA-EKTQVAIVRHFGLQILEHVVKFRWN--------GMSRLEKVYLKNSVMELI',
                str(hsp.query.seq))
        self.assertEqual('56788886699*********.6555899******************........999999****99999887',
                hsp.aln_annotation['PP'])

        hsp = hit.hsps[-1]
        self.assertEqual(2, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(-3.3, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(1.2, hsp.evalue_cond)
        self.assertEqual(8e+03, hsp.evalue)
        self.assertEqual(56, hsp.hit_start)
        self.assertEqual(75, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(167, hsp.query_start)
        self.assertEqual(186, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(164, hsp.env_start)
        self.assertEqual(187, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.85, hsp.acc_avg)
        self.assertEqual('HCS-HHHHHHHHHHHHHHH',
                hsp.aln_annotation['CS'])
        self.assertEqual('qqlpeeekelIrnnllnll',
                str(hsp.hit.seq))
        self.assertEqual('QTLPPQRRRDIQQTLTQNM',
                str(hsp.query.seq))
        self.assertEqual('6899*******99998865',
                hsp.aln_annotation['PP'])

        # test if we've properly finished iteration
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_30_hmmscan_009(self):
        "Test parsing hmmscan 3.0 (text_30_hmmscan_009)"
        hmmer_file = get_file('text_30_hmmscan_009.out')
        qresults = parse(hmmer_file, FMT)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1
        self.assertEqual('SCO3574', qresult.id)
        self.assertEqual(5, len(qresult.hits))
        self.assertEqual('Esterase', qresult.hits[3].id)

    def test_30_hmmscan_010(self):
        "Test parsing hmmscan 3.0 (text_30_hmmscan_010)"
        hmmer_file = get_file('text_30_hmmscan_010.out')
        qresults = list(parse(hmmer_file, FMT))

        # test the Hit object without HSPs
        hit = qresults[0][-1]
        self.assertFalse(hit)
        self.assertEqual('NRPS-COM_Cterm', hit.id)
        self.assertEqual('', hit.description)
        self.assertEqual('bpsA', hit.query_id)
        self.assertEqual('<unknown description>', hit.query_description)
        self.assertEqual(4.4e-11, hit.evalue)
        self.assertEqual(33.6, hit.bitscore)
        self.assertEqual(10.2, hit.bias)
        self.assertEqual(2.9, hit.domain_exp_num)
        self.assertEqual(0, hit.domain_obs_num)
        self.assertEqual(0, len(hit))


class HmmersearchCases(unittest.TestCase):

    def test_31b2_hmmscan_001(self):
        """Test parsing hmmscan 3.1b2 (text_31b2_hmmscan_001)"""

        txt_file = get_file('text_31b2_hmmscan_001.out')
        qresults = list(parse(txt_file, FMT))

        # expects only 1 query result
        self.assertEqual(1, len(qresults))

        # in that query result, there are 108 hits
        qresult = qresults[0]
        self.assertEqual(108, len(qresult))

        # making sure all query IDs are equal
        self.assertEqual("Protein-arginine kinase activator protein "
                         "OS=Bacillus subtilis (strain 168) GN=mcsA "
                         "PE=1 SV=1", qresult.description)

        # and all hits have no descriptions
        for hit in qresult:
            self.assertEqual("", hit.description)

    def test_31b1_hmmsearch_001(self):
        """Test parsing hmmsearch 3.1b1 (text_31b1_hmmsearch_001)"""

        txt_file = get_file('text_31b1_hmmsearch_001.out')
        qresults = list(parse(txt_file, FMT))

        self.assertEqual(2, len(qresults))

        # first qresult is empty
        qresult = qresults[0]
        self.assertEqual('Globins', qresult.id)
        self.assertEqual(149, qresult.seq_len)
        self.assertEqual(0, len(qresult))

        # second qresult
        qresult = qresults[1]
        self.assertEqual('Pkinase', qresult.id)
        self.assertEqual(260, qresult.seq_len)
        self.assertEqual('PF00069.17', qresult.accession)
        self.assertEqual('Protein kinase domain', qresult.description)
        self.assertEqual(4, len(qresult))

        # first hit, first hsp
        hit = qresult[0]
        self.assertEqual('sp|Q9WUT3|KS6A2_MOUSE', hit.id)
        self.assertEqual('Ribosomal protein S6 kinase alpha-2 OS=Mus musculus GN=Rps6ka2 PE=1 SV=1',
                         hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(8.5e-147, hit.evalue)
        self.assertEqual(492.3, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.1, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(241.2, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(2.6e-75, hsp.evalue_cond)
        self.assertEqual(3.6e-70, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(58, hsp.hit_start)
        self.assertEqual(318, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(58, hsp.env_start)
        self.assertEqual(318, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.95, hsp.acc_avg)
        self.assertEqual('EEEEEEEEEETTEEEEEEEE...TTTTEEEEEEEEEHHHCCCCCCHHHHHHHHHHHHHSSSSB--EEEEEEETTEEEEEEE--TS-BHHHHHHHHHST-HHHHHHHHHHHHHHHHHHHHTTEE-S--SGGGEEEETTTEEEE--GTT.E..EECSS-C-S--S-GGGS-HHHHCCS-CTHHHHHHHHHHHHHHHHHHSS-TTSSSHHCCTHHHHSSHHH......TTS.....HHHHHHHHHHT-SSGGGSTT.....HHHHHTSGGG',
                hsp.aln_annotation['CS'])
        self.assertEqual('yelleklGsGsfGkVykakk...kktgkkvAvKilkkeeekskkektavrElkilkklsHpnivkllevfetkdelylvleyveggdlfdllkkegklseeeikkialqilegleylHsngiiHrDLKpeNiLldkkgevkiaDFGlakkleksseklttlvgtreYmAPEvllkakeytkkvDvWslGvilyelltgklpfsgeseedqleliekilkkkleedepkssskseelkdlikkllekdpakRlt.....aeeilkhpwl',
                str(hsp.query.seq))
        self.assertEqual('FELLKVLGQGSYGKVFLVRKvtgSDAGQLYAMKVLKKATLKVRDRVRSKMERDILAEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALALDHLHGLGIIYRDLKPENILLDEEGHIKITDFGLSKEATDHDKRAYSFCGTIEYMAPEVVN-RRGHTQSADWWSFGVLMFEMLTGSLPFQGK---DRKETMALILKAKLGMPQFLS----AEAQSLLRALFKRNPCNRLGagvdgVEEIKRHPFF',
                str(hsp.hit.seq))
        self.assertEqual('67899**********7666611155667*****************99999****************************************************************************************************************************.******************************...999999999999999998866....99******************9999999*****997',
                hsp.aln_annotation['PP'])

    def test_30_hmmsearch_001(self):
        "Test parsing hmmersearch 3.0 (text_30_hmmsearch_001)"

        txt_file = get_file('text_30_hmmsearch_001.out')
        qresults = parse(txt_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmsearch', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/uniprot_sprot.fasta', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('globins4', qresult.id)
        self.assertEqual(149, qresult.seq_len)
        self.assertEqual(0, len(qresult))

        # test if we've properly finished iteration
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(1, counter)

    def test_30_hmmsearch_002(self):
        "Test parsing hmmersearch 3.0 (text_30_hmmsearch_002)"

        txt_file = get_file('text_30_hmmsearch_002.out')
        qresults = parse(txt_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmsearch', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/uniprot_sprot.fasta', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('Pkinase', qresult.id)
        self.assertEqual('PF00069.17', qresult.accession)
        self.assertEqual('Protein kinase domain', qresult.description)
        self.assertEqual(260, qresult.seq_len)
        self.assertEqual(7, len(qresult))

        hit = qresult[0]
        self.assertEqual('sp|Q9WUT3|KS6A2_MOUSE', hit.id)
        self.assertEqual('Ribosomal protein S6 kinase alpha-2 OS=Mus musculus GN=Rps6ka2 PE=2 SV=1',
                         hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(8.4e-147, hit.evalue)
        self.assertEqual(492.3, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.1, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(241.2, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(4.6e-75, hsp.evalue_cond)
        self.assertEqual(3.5e-70, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(58, hsp.hit_start)
        self.assertEqual(318, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(58, hsp.env_start)
        self.assertEqual(318, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.95, hsp.acc_avg)
        self.assertEqual('EEEEEEEEEETTEEEEEEEE...TTTTEEEEEEEEEHHHCCCCCCHHHHHHHHHHHHHSSSSB--EEEEEEETTEEEEEEE--TS-BHHHHHHHHHST-HHHHHHHHHHHHHHHHHHHHTTEE-S--SGGGEEEETTTEEEE--GTT.E..EECSS-C-S--S-GGGS-HHHHCCS-CTHHHHHHHHHHHHHHHHHHSS-TTSSSHHCCTHHHHSSHHH......TTS.....HHHHHHHHHHT-SSGGGSTT.....HHHHHTSGGG',
                hsp.aln_annotation['CS'])
        self.assertEqual('yelleklGsGsfGkVykakk...kktgkkvAvKilkkeeekskkektavrElkilkklsHpnivkllevfetkdelylvleyveggdlfdllkkegklseeeikkialqilegleylHsngiiHrDLKpeNiLldkkgevkiaDFGlakkleksseklttlvgtreYmAPEvllkakeytkkvDvWslGvilyelltgklpfsgeseedqleliekilkkkleedepkssskseelkdlikkllekdpakRlt.....aeeilkhpwl',
                str(hsp.query.seq))
        self.assertEqual('FELLKVLGQGSYGKVFLVRKvtgSDAGQLYAMKVLKKATLKVRDRVRSKMERDILAEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALALDHLHGLGIIYRDLKPENILLDEEGHIKITDFGLSKEATDHDKRAYSFCGTIEYMAPEVVN-RRGHTQSADWWSFGVLMFEMLTGSLPFQGK---DRKETMALILKAKLGMPQFLS----AEAQSLLRALFKRNPCNRLGagvdgVEEIKRHPFF',
                str(hsp.hit.seq))
        self.assertEqual('67899**********7666611155667*****************99999****************************************************************************************************************************.******************************...999999999999999998866....99******************9999999*****997',
                hsp.aln_annotation['PP'])

        hsp = hit.hsps[1]
        self.assertEqual(2, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(249.3, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(1.5e-77, hsp.evalue_cond)
        self.assertEqual(1.1e-72, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(414, hsp.hit_start)
        self.assertEqual(672, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(414, hsp.env_start)
        self.assertEqual(672, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.97, hsp.acc_avg)
        self.assertEqual('EEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEHHHCCCCCCHHHHHHHHHHHHH.SSSSB--EEEEEEETTEEEEEEE--TS-BHHHHHHHHHST-HHHHHHHHHHHHHHHHHHHHTTEE-S--SGGGEEEETTTEE....EE--GTT.E..EECSS-C-S--S-GGGS-HHHHCCS-CTHHHHHHHHHHHHHHHHHHSS-TTSSSHHCCTHHHHSSHHH......TTS.....HHHHHHHHHHT-SSGGGSTTHHHHHTSGGG',
                hsp.aln_annotation['CS'])
        self.assertEqual('yelleklGsGsfGkVykakkkktgkkvAvKilkkeeekskkektavrElkilkkl.sHpnivkllevfetkdelylvleyveggdlfdllkkegklseeeikkialqilegleylHsngiiHrDLKpeNiLldkkgev....kiaDFGlakkleksseklttlvgtreYmAPEvllkakeytkkvDvWslGvilyelltgklpfsgeseedqleliekilkkkleedepkssskseelkdlikkllekdpakRltaeeilkhpwl',
                str(hsp.query.seq))
        self.assertEqual('YEIKEDIGVGSYSVCKRCVHKATDAEYAVKIIDKSKRDPSE------EIEILLRYgQHPNIITLKDVYDDGKYVYLVMELMRGGELLDRILRQRCFSEREASDVLYTIARTMDYLHSQGVVHRDLKPSNILYMDESGNpesiRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLK-RQGYDAACDVWSLGILLYTMLAGFTPFANGPDDTPEEILARIGSGKYALSGGNWDSISDAAKDVVSKMLHVDPQQRLTAVQVLKHPWI',
                str(hsp.hit.seq))
        self.assertEqual('7899***********************************98......9*******99**************************************************************************98544444888**********************************.***************************************************************************************7',
                hsp.aln_annotation['PP'])

        hit = qresult[-1]
        self.assertEqual('sp|P18654|KS6A3_MOUSE', hit.id)
        self.assertEqual('Ribosomal protein S6 kinase alpha-3 OS=Mus musculus GN=Rps6ka3 PE=1 SV=2',
                         hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(5e-144, hit.evalue)
        self.assertEqual(483.2, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.2, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(240.3, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(8.7e-75, hsp.evalue_cond)
        self.assertEqual(6.6e-70, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(67, hsp.hit_start)
        self.assertEqual(327, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(67, hsp.env_start)
        self.assertEqual(327, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.95, hsp.acc_avg)
        self.assertEqual('EEEEEEEEEETTEEEEEEEETTTTE...EEEEEEEEHHHCCCCCCHHHHHHHHHHHHHSSSSB--EEEEEEETTEEEEEEE--TS-BHHHHHHHHHST-HHHHHHHHHHHHHHHHHHHHTTEE-S--SGGGEEEETTTEEEE--GTT.E..EECSS-C-S--S-GGGS-HHHHCCS-CTHHHHHHHHHHHHHHHHHHSS-TTSSSHHCCTHHHHSSHHH......TTS.....HHHHHHHHHHT-SSGGGSTT.....HHHHHTSGGG',
                hsp.aln_annotation['CS'])
        self.assertEqual('yelleklGsGsfGkVykakkkktgk...kvAvKilkkeeekskkektavrElkilkklsHpnivkllevfetkdelylvleyveggdlfdllkkegklseeeikkialqilegleylHsngiiHrDLKpeNiLldkkgevkiaDFGlakkleksseklttlvgtreYmAPEvllkakeytkkvDvWslGvilyelltgklpfsgeseedqleliekilkkkleedepkssskseelkdlikkllekdpakRlt.....aeeilkhpwl',
                str(hsp.query.seq))
        self.assertEqual('FELLKVLGQGSFGKVFLVKKISGSDarqLYAMKVLKKATLKVRDRVRTKMERDILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALALDHLHSLGIIYRDLKPENILLDEEGHIKLTDFGLSKESIDHEKKAYSFCGTVEYMAPEVVN-RRGHTQSADWWSFGVLMFEMLTGTLPFQGK---DRKETMTMILKAKLGMPQFLS----PEAQSLLRMLFKRNPANRLGagpdgVEEIKRHSFF',
                str(hsp.hit.seq))
        self.assertEqual('67899**********8888876655455****************999999****************************************************************************************************9***********************.******************************...999999999999988888866....9******************9888888999999886',
                hsp.aln_annotation['PP'])

        hsp = hit.hsps[1]
        self.assertEqual(2, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(241.0, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(5.1e-75, hsp.evalue_cond)
        self.assertEqual(3.9e-70, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(421, hsp.hit_start)
        self.assertEqual(679, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(421, hsp.env_start)
        self.assertEqual(679, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.97, hsp.acc_avg)
        self.assertEqual('EEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEHHHCCCCCCHHHHHHHHHHHHH.SSSSB--EEEEEEETTEEEEEEE--TS-BHHHHHHHHHST-HHHHHHHHHHHHHHHHHHHHTTEE-S--SGGGEEEETTTEE....EE--GTT.E..EECSS-C-S--S-GGGS-HHHHCCS-CTHHHHHHHHHHHHHHHHHHSS-TTSSSHHCCTHHHHSSHHH......TTS.....HHHHHHHHHHT-SSGGGSTTHHHHHTSGGG',
                hsp.aln_annotation['CS'])
        self.assertEqual('yelleklGsGsfGkVykakkkktgkkvAvKilkkeeekskkektavrElkilkkl.sHpnivkllevfetkdelylvleyveggdlfdllkkegklseeeikkialqilegleylHsngiiHrDLKpeNiLldkkgev....kiaDFGlakkleksseklttlvgtreYmAPEvllkakeytkkvDvWslGvilyelltgklpfsgeseedqleliekilkkkleedepkssskseelkdlikkllekdpakRltaeeilkhpwl',
                str(hsp.query.seq))
        self.assertEqual('YEVKEDIGVGSYSVCKRCIHKATNMEFAVKIIDKSKRDPTE------EIEILLRYgQHPNIITLKDVYDDGKYVYVVTELMKGGELLDKILRQKFFSEREASAVLFTITKTVEYLHAQGVVHRDLKPSNILYVDESGNpesiRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLK-RQGYDAACDIWSLGVLLYTMLTGYTPFANGPDDTPEEILARIGSGKFSLSGGYWNSVSDTAKDLVSKMLHVDPHQRLTAALVLRHPWI',
                str(hsp.hit.seq))
        self.assertEqual('7899***********************************88......9*******99**********************************9***************************************98554444888**********************************.***************************************************************************************7',
                hsp.aln_annotation['PP'])

        # test if we've properly finished iteration
        # self.assertRaises(StopIteration, next, qresults)
        # self.assertEqual(1, counter)

    def test_30_hmmsearch_003(self):
        "Test parsing hmmersearch 3.0 (text_30_hmmsearch_003)"

        txt_file = get_file('text_30_hmmsearch_003.out')
        qresults = parse(txt_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmsearch', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/uniprot_sprot.fasta', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('Pkinase', qresult.id)
        self.assertEqual('PF00069.17', qresult.accession)
        self.assertEqual('Protein kinase domain', qresult.description)
        self.assertEqual(260, qresult.seq_len)
        self.assertEqual(7, len(qresult))

        hit = qresult[0]
        self.assertEqual('sp|Q9WUT3|KS6A2_MOUSE', hit.id)
        self.assertEqual('Ribosomal protein S6 kinase alpha-2 OS=Mus musculus GN=Rps6ka2 PE=2 SV=1',
                         hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(8.4e-147, hit.evalue)
        self.assertEqual(492.3, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.1, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(241.2, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(4.6e-75, hsp.evalue_cond)
        self.assertEqual(3.5e-70, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(58, hsp.hit_start)
        self.assertEqual(318, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(58, hsp.env_start)
        self.assertEqual(318, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.95, hsp.acc_avg)

        hsp = hit.hsps[1]
        self.assertEqual(2, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(249.3, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(1.5e-77, hsp.evalue_cond)
        self.assertEqual(1.1e-72, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(414, hsp.hit_start)
        self.assertEqual(672, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(414, hsp.env_start)
        self.assertEqual(672, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.97, hsp.acc_avg)

        hit = qresult[-1]
        self.assertEqual('sp|P18654|KS6A3_MOUSE', hit.id)
        self.assertEqual('Ribosomal protein S6 kinase alpha-3 OS=Mus musculus GN=Rps6ka3 PE=1 SV=2',
                         hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(5e-144, hit.evalue)
        self.assertEqual(483.2, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.2, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(240.3, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(8.7e-75, hsp.evalue_cond)
        self.assertEqual(6.6e-70, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(67, hsp.hit_start)
        self.assertEqual(327, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(67, hsp.env_start)
        self.assertEqual(327, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.95, hsp.acc_avg)

        hsp = hit.hsps[1]
        self.assertEqual(2, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(241.0, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(5.1e-75, hsp.evalue_cond)
        self.assertEqual(3.9e-70, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(421, hsp.hit_start)
        self.assertEqual(679, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(421, hsp.env_start)
        self.assertEqual(679, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.97, hsp.acc_avg)

        # test if we've properly finished iteration
        # self.assertRaises(StopIteration, next, qresults)
        # self.assertEqual(1, counter)

    def test_30_hmmsearch_004(self):
        "Test parsing hmmersearch 3.0 (text_30_hmmsearch_004)"

        txt_file = get_file('text_30_hmmsearch_004.out')
        qresults = parse(txt_file, FMT)
        counter = 0

        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmsearch', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/uniprot_sprot.fasta', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('Pkinase', qresult.id)
        self.assertEqual('PF00069.17', qresult.accession)
        self.assertEqual('Protein kinase domain', qresult.description)
        self.assertEqual(260, qresult.seq_len)
        self.assertEqual(7, len(qresult))

        hit = qresult[0]
        self.assertEqual('sp|Q9WUT3|KS6A2_MOUSE', hit.id)
        self.assertEqual('Ribosomal protein S6 kinase alpha-2 OS=Mus musculus GN=Rps6ka2 PE=2 SV=1',
                         hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(8.4e-147, hit.evalue)
        self.assertEqual(492.3, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.1, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(241.2, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(4.6e-75, hsp.evalue_cond)
        self.assertEqual(3.5e-70, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(58, hsp.hit_start)
        self.assertEqual(318, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(58, hsp.env_start)
        self.assertEqual(318, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.95, hsp.acc_avg)
        self.assertEqual('EEEEEEEEEETTEEEEEEEE...TTTTEEEEEEEEEHHHCCCCCCHHHHHHHHHHHHHSSSSB--EEEEEEETTEEEEEEE--TS-BHHHHHHHHHST-HHHHHHHHHHHHHHHHHHHHTTEE-S--SGGGEEEETTTEEEE--GTT.E..EECSS-C-S--S-GGGS-HHHHCCS-CTHHHHHHHHHHHHHHHHHHSS-TTSSSHHCCTHHHHSSHHH......TTS.....HHHHHHHHHHT-SSGGGSTT.....HHHHHTSGGG',
                hsp.aln_annotation['CS'])
        self.assertEqual('yelleklGsGsfGkVykakk...kktgkkvAvKilkkeeekskkektavrElkilkklsHpnivkllevfetkdelylvleyveggdlfdllkkegklseeeikkialqilegleylHsngiiHrDLKpeNiLldkkgevkiaDFGlakkleksseklttlvgtreYmAPEvllkakeytkkvDvWslGvilyelltgklpfsgeseedqleliekilkkkleedepkssskseelkdlikkllekdpakRlt.....aeeilkhpwl',
                str(hsp.query.seq))
        self.assertEqual('FELLKVLGQGSYGKVFLVRKvtgSDAGQLYAMKVLKKATLKVRDRVRSKMERDILAEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALALDHLHGLGIIYRDLKPENILLDEEGHIKITDFGLSKEATDHDKRAYSFCGTIEYMAPEVVN-RRGHTQSADWWSFGVLMFEMLTGSLPFQGK---DRKETMALILKAKLGMPQFLS----AEAQSLLRALFKRNPCNRLGagvdgVEEIKRHPFF',
                str(hsp.hit.seq))
        self.assertEqual('67899**********7666611155667*****************99999****************************************************************************************************************************.******************************...999999999999999998866....99******************9999999*****997',
                hsp.aln_annotation['PP'])

        hsp = hit.hsps[1]
        self.assertEqual(2, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(249.3, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(1.5e-77, hsp.evalue_cond)
        self.assertEqual(1.1e-72, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(414, hsp.hit_start)
        self.assertEqual(672, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(414, hsp.env_start)
        self.assertEqual(672, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.97, hsp.acc_avg)
        self.assertEqual('EEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEHHHCCCCCCHHHHHHHHHHHHH.SSSSB--EEEEEEETTEEEEEEE--TS-BHHHHHHHHHST-HHHHHHHHHHHHHHHHHHHHTTEE-S--SGGGEEEETTTEE....EE--GTT.E..EECSS-C-S--S-GGGS-HHHHCCS-CTHHHHHHHHHHHHHHHHHHSS-TTSSSHHCCTHHHHSSHHH......TTS.....HHHHHHHHHHT-SSGGGSTTHHHHHTSGGG',
                hsp.aln_annotation['CS'])
        self.assertEqual('yelleklGsGsfGkVykakkkktgkkvAvKilkkeeekskkektavrElkilkkl.sHpnivkllevfetkdelylvleyveggdlfdllkkegklseeeikkialqilegleylHsngiiHrDLKpeNiLldkkgev....kiaDFGlakkleksseklttlvgtreYmAPEvllkakeytkkvDvWslGvilyelltgklpfsgeseedqleliekilkkkleedepkssskseelkdlikkllekdpakRltaeeilkhpwl',
                str(hsp.query.seq))
        self.assertEqual('YEIKEDIGVGSYSVCKRCVHKATDAEYAVKIIDKSKRDPSE------EIEILLRYgQHPNIITLKDVYDDGKYVYLVMELMRGGELLDRILRQRCFSEREASDVLYTIARTMDYLHSQGVVHRDLKPSNILYMDESGNpesiRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLK-RQGYDAACDVWSLGILLYTMLAGFTPFANGPDDTPEEILARIGSGKYALSGGNWDSISDAAKDVVSKMLHVDPQQRLTAVQVLKHPWI',
                str(hsp.hit.seq))
        self.assertEqual('7899***********************************98......9*******99**************************************************************************98544444888**********************************.***************************************************************************************7',
                hsp.aln_annotation['PP'])

        hit = qresult[-1]
        self.assertEqual('sp|P18654|KS6A3_MOUSE', hit.id)
        self.assertEqual('Ribosomal protein S6 kinase alpha-3 OS=Mus musculus GN=Rps6ka3 PE=1 SV=2',
                         hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(5e-144, hit.evalue)
        self.assertEqual(483.2, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.2, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(240.3, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(8.7e-75, hsp.evalue_cond)
        self.assertEqual(6.6e-70, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(67, hsp.hit_start)
        self.assertEqual(327, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(67, hsp.env_start)
        self.assertEqual(327, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.95, hsp.acc_avg)
        self.assertEqual('EEEEEEEEEETTEEEEEEEETTTTE...EEEEEEEEHHHCCCCCCHHHHHHHHHHHHHSSSSB--EEEEEEETTEEEEEEE--TS-BHHHHHHHHHST-HHHHHHHHHHHHHHHHHHHHTTEE-S--SGGGEEEETTTEEEE--GTT.E..EECSS-C-S--S-GGGS-HHHHCCS-CTHHHHHHHHHHHHHHHHHHSS-TTSSSHHCCTHHHHSSHHH......TTS.....HHHHHHHHHHT-SSGGGSTT.....HHHHHTSGGG',
                hsp.aln_annotation['CS'])
        self.assertEqual('yelleklGsGsfGkVykakkkktgk...kvAvKilkkeeekskkektavrElkilkklsHpnivkllevfetkdelylvleyveggdlfdllkkegklseeeikkialqilegleylHsngiiHrDLKpeNiLldkkgevkiaDFGlakkleksseklttlvgtreYmAPEvllkakeytkkvDvWslGvilyelltgklpfsgeseedqleliekilkkkleedepkssskseelkdlikkllekdpakRlt.....aeeilkhpwl',
                str(hsp.query.seq))
        self.assertEqual('FELLKVLGQGSFGKVFLVKKISGSDarqLYAMKVLKKATLKVRDRVRTKMERDILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALALDHLHSLGIIYRDLKPENILLDEEGHIKLTDFGLSKESIDHEKKAYSFCGTVEYMAPEVVN-RRGHTQSADWWSFGVLMFEMLTGTLPFQGK---DRKETMTMILKAKLGMPQFLS----PEAQSLLRMLFKRNPANRLGagpdgVEEIKRHSFF',
                str(hsp.hit.seq))
        self.assertEqual('67899**********8888876655455****************999999****************************************************************************************************9***********************.******************************...999999999999988888866....9******************9888888999999886',
                hsp.aln_annotation['PP'])

        hsp = hit.hsps[1]
        self.assertEqual(2, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(241.0, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(5.1e-75, hsp.evalue_cond)
        self.assertEqual(3.9e-70, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(421, hsp.hit_start)
        self.assertEqual(679, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(421, hsp.env_start)
        self.assertEqual(679, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.97, hsp.acc_avg)
        self.assertEqual('EEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEHHHCCCCCCHHHHHHHHHHHHH.SSSSB--EEEEEEETTEEEEEEE--TS-BHHHHHHHHHST-HHHHHHHHHHHHHHHHHHHHTTEE-S--SGGGEEEETTTEE....EE--GTT.E..EECSS-C-S--S-GGGS-HHHHCCS-CTHHHHHHHHHHHHHHHHHHSS-TTSSSHHCCTHHHHSSHHH......TTS.....HHHHHHHHHHT-SSGGGSTTHHHHHTSGGG',
                hsp.aln_annotation['CS'])
        self.assertEqual('yelleklGsGsfGkVykakkkktgkkvAvKilkkeeekskkektavrElkilkkl.sHpnivkllevfetkdelylvleyveggdlfdllkkegklseeeikkialqilegleylHsngiiHrDLKpeNiLldkkgev....kiaDFGlakkleksseklttlvgtreYmAPEvllkakeytkkvDvWslGvilyelltgklpfsgeseedqleliekilkkkleedepkssskseelkdlikkllekdpakRltaeeilkhpwl',
                str(hsp.query.seq))
        self.assertEqual('YEVKEDIGVGSYSVCKRCIHKATNMEFAVKIIDKSKRDPTE------EIEILLRYgQHPNIITLKDVYDDGKYVYVVTELMKGGELLDKILRQKFFSEREASAVLFTITKTVEYLHAQGVVHRDLKPSNILYVDESGNpesiRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLK-RQGYDAACDIWSLGVLLYTMLTGYTPFANGPDDTPEEILARIGSGKFSLSGGYWNSVSDTAKDLVSKMLHVDPHQRLTAALVLRHPWI',
                str(hsp.hit.seq))
        self.assertEqual('7899***********************************88......9*******99**********************************9***************************************98554444888**********************************.***************************************************************************************7',
                hsp.aln_annotation['PP'])

        # test if we've properly finished iteration
        # self.assertRaises(StopIteration, next, qresults)
        # self.assertEqual(1, counter)

    def test_30_hmmsearch_005(self):
        "Test parsing hmmersearch 3.0 (text_30_hmmsearch_005)"

        txt_file = get_file('text_30_hmmsearch_005.out')
        qresults = parse(txt_file, FMT)
        counter = 0

        # test first qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmsearch', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/uniprot_sprot.fasta', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('globins4', qresult.id)
        self.assertEqual(149, qresult.seq_len)
        self.assertEqual(0, len(qresult))

        # test second qresult
        qresult = next(qresults)
        counter += 1

        self.assertEqual('hmmsearch', qresult.program)
        self.assertEqual('/home/bow/db/hmmer/uniprot_sprot.fasta', qresult.target)
        self.assertEqual('3.0', qresult.version)
        self.assertEqual('Pkinase', qresult.id)
        self.assertEqual('PF00069.17', qresult.accession)
        self.assertEqual('Protein kinase domain', qresult.description)
        self.assertEqual(260, qresult.seq_len)
        self.assertEqual(7, len(qresult))

        hit = qresult[0]
        self.assertEqual('sp|Q9WUT3|KS6A2_MOUSE', hit.id)
        self.assertEqual('Ribosomal protein S6 kinase alpha-2 OS=Mus musculus GN=Rps6ka2 PE=2 SV=1',
                         hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(8.4e-147, hit.evalue)
        self.assertEqual(492.3, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.1, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(241.2, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(4.6e-75, hsp.evalue_cond)
        self.assertEqual(3.5e-70, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(58, hsp.hit_start)
        self.assertEqual(318, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(58, hsp.env_start)
        self.assertEqual(318, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.95, hsp.acc_avg)
        self.assertEqual('EEEEEEEEEETTEEEEEEEE...TTTTEEEEEEEEEHHHCCCCCCHHHHHHHHHHHHHSSSSB--EEEEEEETTEEEEEEE--TS-BHHHHHHHHHST-HHHHHHHHHHHHHHHHHHHHTTEE-S--SGGGEEEETTTEEEE--GTT.E..EECSS-C-S--S-GGGS-HHHHCCS-CTHHHHHHHHHHHHHHHHHHSS-TTSSSHHCCTHHHHSSHHH......TTS.....HHHHHHHHHHT-SSGGGSTT.....HHHHHTSGGG',
                hsp.aln_annotation['CS'])
        self.assertEqual('yelleklGsGsfGkVykakk...kktgkkvAvKilkkeeekskkektavrElkilkklsHpnivkllevfetkdelylvleyveggdlfdllkkegklseeeikkialqilegleylHsngiiHrDLKpeNiLldkkgevkiaDFGlakkleksseklttlvgtreYmAPEvllkakeytkkvDvWslGvilyelltgklpfsgeseedqleliekilkkkleedepkssskseelkdlikkllekdpakRlt.....aeeilkhpwl',
                str(hsp.query.seq))
        self.assertEqual('FELLKVLGQGSYGKVFLVRKvtgSDAGQLYAMKVLKKATLKVRDRVRSKMERDILAEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALALDHLHGLGIIYRDLKPENILLDEEGHIKITDFGLSKEATDHDKRAYSFCGTIEYMAPEVVN-RRGHTQSADWWSFGVLMFEMLTGSLPFQGK---DRKETMALILKAKLGMPQFLS----AEAQSLLRALFKRNPCNRLGagvdgVEEIKRHPFF',
                str(hsp.hit.seq))
        self.assertEqual('67899**********7666611155667*****************99999****************************************************************************************************************************.******************************...999999999999999998866....99******************9999999*****997',
                hsp.aln_annotation['PP'])

        hsp = hit.hsps[1]
        self.assertEqual(2, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(249.3, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(1.5e-77, hsp.evalue_cond)
        self.assertEqual(1.1e-72, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(414, hsp.hit_start)
        self.assertEqual(672, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(414, hsp.env_start)
        self.assertEqual(672, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.97, hsp.acc_avg)
        self.assertEqual('EEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEHHHCCCCCCHHHHHHHHHHHHH.SSSSB--EEEEEEETTEEEEEEE--TS-BHHHHHHHHHST-HHHHHHHHHHHHHHHHHHHHTTEE-S--SGGGEEEETTTEE....EE--GTT.E..EECSS-C-S--S-GGGS-HHHHCCS-CTHHHHHHHHHHHHHHHHHHSS-TTSSSHHCCTHHHHSSHHH......TTS.....HHHHHHHHHHT-SSGGGSTTHHHHHTSGGG',
                hsp.aln_annotation['CS'])
        self.assertEqual('yelleklGsGsfGkVykakkkktgkkvAvKilkkeeekskkektavrElkilkkl.sHpnivkllevfetkdelylvleyveggdlfdllkkegklseeeikkialqilegleylHsngiiHrDLKpeNiLldkkgev....kiaDFGlakkleksseklttlvgtreYmAPEvllkakeytkkvDvWslGvilyelltgklpfsgeseedqleliekilkkkleedepkssskseelkdlikkllekdpakRltaeeilkhpwl',
                str(hsp.query.seq))
        self.assertEqual('YEIKEDIGVGSYSVCKRCVHKATDAEYAVKIIDKSKRDPSE------EIEILLRYgQHPNIITLKDVYDDGKYVYLVMELMRGGELLDRILRQRCFSEREASDVLYTIARTMDYLHSQGVVHRDLKPSNILYMDESGNpesiRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLK-RQGYDAACDVWSLGILLYTMLAGFTPFANGPDDTPEEILARIGSGKYALSGGNWDSISDAAKDVVSKMLHVDPQQRLTAVQVLKHPWI',
                str(hsp.hit.seq))
        self.assertEqual('7899***********************************98......9*******99**************************************************************************98544444888**********************************.***************************************************************************************7',
                hsp.aln_annotation['PP'])

        hit = qresult[-1]
        self.assertEqual('sp|P18654|KS6A3_MOUSE', hit.id)
        self.assertEqual('Ribosomal protein S6 kinase alpha-3 OS=Mus musculus GN=Rps6ka3 PE=1 SV=2',
                         hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(5e-144, hit.evalue)
        self.assertEqual(483.2, hit.bitscore)
        self.assertEqual(0.0, hit.bias)
        self.assertEqual(2.2, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(240.3, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(8.7e-75, hsp.evalue_cond)
        self.assertEqual(6.6e-70, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(67, hsp.hit_start)
        self.assertEqual(327, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(67, hsp.env_start)
        self.assertEqual(327, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.95, hsp.acc_avg)
        self.assertEqual('EEEEEEEEEETTEEEEEEEETTTTE...EEEEEEEEHHHCCCCCCHHHHHHHHHHHHHSSSSB--EEEEEEETTEEEEEEE--TS-BHHHHHHHHHST-HHHHHHHHHHHHHHHHHHHHTTEE-S--SGGGEEEETTTEEEE--GTT.E..EECSS-C-S--S-GGGS-HHHHCCS-CTHHHHHHHHHHHHHHHHHHSS-TTSSSHHCCTHHHHSSHHH......TTS.....HHHHHHHHHHT-SSGGGSTT.....HHHHHTSGGG',
                hsp.aln_annotation['CS'])
        self.assertEqual('yelleklGsGsfGkVykakkkktgk...kvAvKilkkeeekskkektavrElkilkklsHpnivkllevfetkdelylvleyveggdlfdllkkegklseeeikkialqilegleylHsngiiHrDLKpeNiLldkkgevkiaDFGlakkleksseklttlvgtreYmAPEvllkakeytkkvDvWslGvilyelltgklpfsgeseedqleliekilkkkleedepkssskseelkdlikkllekdpakRlt.....aeeilkhpwl',
                str(hsp.query.seq))
        self.assertEqual('FELLKVLGQGSFGKVFLVKKISGSDarqLYAMKVLKKATLKVRDRVRTKMERDILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALALDHLHSLGIIYRDLKPENILLDEEGHIKLTDFGLSKESIDHEKKAYSFCGTVEYMAPEVVN-RRGHTQSADWWSFGVLMFEMLTGTLPFQGK---DRKETMTMILKAKLGMPQFLS----PEAQSLLRMLFKRNPANRLGagpdgVEEIKRHSFF',
                str(hsp.hit.seq))
        self.assertEqual('67899**********8888876655455****************999999****************************************************************************************************9***********************.******************************...999999999999988888866....9******************9888888999999886',
                hsp.aln_annotation['PP'])

        hsp = hit.hsps[1]
        self.assertEqual(2, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(241.0, hsp.bitscore)
        self.assertEqual(0.0, hsp.bias)
        self.assertEqual(5.1e-75, hsp.evalue_cond)
        self.assertEqual(3.9e-70, hsp.evalue)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(260, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(421, hsp.hit_start)
        self.assertEqual(679, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(421, hsp.env_start)
        self.assertEqual(679, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.97, hsp.acc_avg)
        self.assertEqual('EEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEHHHCCCCCCHHHHHHHHHHHHH.SSSSB--EEEEEEETTEEEEEEE--TS-BHHHHHHHHHST-HHHHHHHHHHHHHHHHHHHHTTEE-S--SGGGEEEETTTEE....EE--GTT.E..EECSS-C-S--S-GGGS-HHHHCCS-CTHHHHHHHHHHHHHHHHHHSS-TTSSSHHCCTHHHHSSHHH......TTS.....HHHHHHHHHHT-SSGGGSTTHHHHHTSGGG',
                hsp.aln_annotation['CS'])
        self.assertEqual('yelleklGsGsfGkVykakkkktgkkvAvKilkkeeekskkektavrElkilkkl.sHpnivkllevfetkdelylvleyveggdlfdllkkegklseeeikkialqilegleylHsngiiHrDLKpeNiLldkkgev....kiaDFGlakkleksseklttlvgtreYmAPEvllkakeytkkvDvWslGvilyelltgklpfsgeseedqleliekilkkkleedepkssskseelkdlikkllekdpakRltaeeilkhpwl',
                str(hsp.query.seq))
        self.assertEqual('YEVKEDIGVGSYSVCKRCIHKATNMEFAVKIIDKSKRDPTE------EIEILLRYgQHPNIITLKDVYDDGKYVYVVTELMKGGELLDKILRQKFFSEREASAVLFTITKTVEYLHAQGVVHRDLKPSNILYVDESGNpesiRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLK-RQGYDAACDIWSLGVLLYTMLTGYTPFANGPDDTPEEILARIGSGKFSLSGGYWNSVSDTAKDLVSKMLHVDPHQRLTAALVLRHPWI',
                str(hsp.hit.seq))
        self.assertEqual('7899***********************************88......9*******99**********************************9***************************************98554444888**********************************.***************************************************************************************7',
                hsp.aln_annotation['PP'])

        # test if we've properly finished iteration
        self.assertRaises(StopIteration, next, qresults)
        self.assertEqual(2, counter)


class PhmmerCases(unittest.TestCase):

    def test_31b2_phmmer_001(self):
        "Test parsing phmmer 3.1b2 (text_31b2_phmmer_001)"

        txt_file = get_file('text_31b2_phmmer_001.out')
        qresults = list(parse(txt_file, FMT))

        # first qresult
        qresult = qresults[0]

        self.assertEqual('phmmer', qresult.program)
        self.assertEqual('/home/bow/devel/sandbox/biopython-sandbox/db/hmmer/protdb/uniprot_sprot.fasta',
                         qresult.target)
        self.assertEqual('3.1b2', qresult.version)
        self.assertEqual('sp|Q6GZX4|001R_FRG3G', qresult.id)
        self.assertEqual(256, qresult.seq_len)
        self.assertEqual(13, len(qresult))

        hit = qresult[0]
        self.assertEqual('sp|Q6GZX4|001R_FRG3G', hit.id)
        self.assertEqual('Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) GN=FV3-001R PE=4 SV=1',
                         hit.description)
        self.assertTrue(hit.is_included)
        self.assertEqual(1.1e-176, hit.evalue)
        self.assertEqual(590.0, hit.bitscore)
        self.assertEqual(1.4, hit.bias)
        self.assertEqual(1.0, hit.domain_exp_num)
        self.assertEqual(1, hit.domain_obs_num)
        self.assertEqual(1, len(hit))

        hsp = hit.hsps[0]
        self.assertEqual(1, hsp.domain_index)
        self.assertTrue(hsp.is_included)
        self.assertEqual(589.9, hsp.bitscore)
        self.assertEqual(1.4, hsp.bias)
        self.assertEqual(3e-181, hsp.evalue_cond)
        self.assertEqual(1.3e-176, hsp.evalue)
        self.assertEqual(0, hsp.hit_start)
        self.assertEqual(256, hsp.hit_end)
        self.assertEqual('[]', hsp.hit_endtype)
        self.assertEqual(0, hsp.query_start)
        self.assertEqual(256, hsp.query_end)
        self.assertEqual('[]', hsp.query_endtype)
        self.assertEqual(0, hsp.env_start)
        self.assertEqual(256, hsp.env_end)
        self.assertEqual('[]', hsp.env_endtype)
        self.assertEqual(1.00, hsp.acc_avg)
        self.assertEqual('mafsaedvlkeydrrrrmealllslyypndrklldykewspprvqvecpkapvewnnppsekglivghfsgikykgekaqasevdvnkm',
                str(hsp.query.seq)[:89])
        self.assertEqual('MAFSAEDVLKEYDRRRRMEALLLSLYYPNDRKLLDYKEWSPPRVQVECPKAPVEWNNPPSEKGLIVGHFSGIKYKGEKAQASEVDVNKM',
                str(hsp.hit.seq)[:89])
        self.assertEqual('89***************************************************************************************',
                hsp.aln_annotation['PP'][:89])

        # last query, last hit
        qresult = qresults[-1]

        self.assertEqual('phmmer', qresult.program)
        self.assertEqual('/home/bow/devel/sandbox/biopython-sandbox/db/hmmer/protdb/uniprot_sprot.fasta',
                         qresult.target)
        self.assertEqual('3.1b2', qresult.version)
        self.assertEqual('sp|Q197F7|003L_IIV3', qresult.id)
        self.assertEqual(156, qresult.seq_len)
        self.assertEqual(6, len(qresult))

        hit = qresult[-1]
        self.assertEqual('sp|P04060|RNAS1_HYSCR', hit.id)
        self.assertEqual('Ribonuclease pancreatic OS=Hystrix cristata GN=RNASE1 PE=1 SV=1', hit.description)
        self.assertFalse(hit.is_included)
        self.assertEqual(2.1, hit.evalue)
        self.assertEqual(13.1, hit.bitscore)
        self.assertEqual(0.7, hit.bias)
        self.assertEqual(1.8, hit.domain_exp_num)
        self.assertEqual(2, hit.domain_obs_num)
        self.assertEqual(2, len(hit))

        hsp = hit.hsps[-1]
        self.assertEqual(2, hsp.domain_index)
        self.assertFalse(hsp.is_included)
        self.assertEqual(12.1, hsp.bitscore)
        self.assertEqual(0.1, hsp.bias)
        self.assertEqual(4.7e-05, hsp.evalue_cond)
        self.assertEqual(4.2, hsp.evalue)
        self.assertEqual(91, hsp.hit_start)
        self.assertEqual(121, hsp.hit_end)
        self.assertEqual('..', hsp.hit_endtype)
        self.assertEqual(7, hsp.query_start)
        self.assertEqual(37, hsp.query_end)
        self.assertEqual('..', hsp.query_endtype)
        self.assertEqual(84, hsp.env_start)
        self.assertEqual(127, hsp.env_end)
        self.assertEqual('..', hsp.env_endtype)
        self.assertEqual(0.84, hsp.acc_avg)
        self.assertEqual('cpqswygspqlereivckmsgaphypnyyp',
                str(hsp.query.seq))
        self.assertEqual('YPDCSYGMSQLERSIVVACEGSPYVPVHFD',
                str(hsp.hit.seq))
        self.assertEqual('68889******************9887764',
                hsp.aln_annotation['PP'])


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)