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#!/usr/bin/env python
# test_infernal.py
from cogent.util.unit_test import TestCase, main
from cogent.parse.infernal import CmsearchParser,CmalignScoreParser
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Development"
class CmsearchParserTests(TestCase):
"""Tests for CmsearchParser.
"""
def setUp(self):
"""setup for CmsearchParserTests.
"""
self.basic_results_empty = """# command data
# date
# CM summary
# Post search summary
"""
self.basic_results_hits = """# command data
# date
# CM summary
Model_1 Target_1 1 10 1 10 25.25 - 50
Model_1 Target_2 3 13 1 10 14.2 - 49
# Post search summary
"""
self.basic_res = [['Model_1','Target_1', 1, 10, 1, 10, 25.25, '-', 50],\
['Model_1','Target_2', 3, 13, 1, 10, 14.2, '-', 49]]
self.search_res = [['model1.cm','seq_0', 5, 23, 1, 19, 12.85, '-', 37],\
['model1.cm','seq_1', 1, 19, 1, 19, 14.36, '-', 47]]
def test_cmsearch_parser_no_data(self):
"""CmsearchParser should return correct result given no data.
"""
parser = CmsearchParser([])
self.assertEqual(list(parser),[])
def test_cmsearch_parser_no_res(self):
"""CmsearchParser should return correct result given no hits in result.
"""
parser = CmsearchParser(self.basic_results_empty.split('\n'))
self.assertEqual(list(parser),[])
def test_cmsearch_parser_basic(self):
"""CmsearchParser should return correct result given basic output.
"""
parser = CmsearchParser(self.basic_results_hits.split('\n'))
self.assertEqual(list(parser),self.basic_res)
def test_cmsearch_parser_full(self):
"""CmsearchParser should return correct result given cmsearch output.
"""
parser = CmsearchParser(SEARCH_DATA.split('\n'))
self.assertEqual(list(parser),self.search_res)
class CmalignScoreParserTests(TestCase):
"""Tests for CmalignScoreParser.
"""
def setUp(self):
"""setup for CmalignScoreParserTests.
"""
self.basic_results_hits = """# command: data
# date:
#
# cm summary
1 Target_1 83 55.02 2.94 0.956 00:00:00.01
2 Target_2 84 53.31 4.42 0.960 00:00:00.01
# post alignment summary
"""
self.basic_res = [[1,'Target_1',83,55.02,2.94,0.956,'00:00:00.01'],\
[2,'Target_2',84,53.31,4.42,0.960,'00:00:00.01']]
self.search_res = \
[[1,'AABL01002928.1/2363-2445',83,55.02,2.94,0.956,'00:00:00.01'],\
[2,'AACV01025780.1/26051-26134',84,53.31,4.42,0.960,'00:00:00.01']]
def test_cmalign_score_parser_no_data(self):
"""CmalignScoreParser should return correct result given no data.
"""
parser = CmalignScoreParser([])
self.assertEqual(list(parser),[])
def test_cmalign_score_parser_basic(self):
"""CmalignScoreParser should return correct result given basic output.
"""
parser = CmalignScoreParser(self.basic_results_hits.split('\n'))
self.assertEqual(list(parser),self.basic_res)
def test_cmalign_score_parser_full(self):
"""CmalignScoreParser should return correct result given cmalign output.
"""
parser = CmalignScoreParser(ALIGN_DATA.split('\n'))
self.assertEqual(list(parser),self.search_res)
SEARCH_DATA = """# command: cmsearch -T 0.0 --tabfile /tmp/tmpQGr0PGVeaEvGUkw2TM3e.txt --informat FASTA /tmp/tmp40hq0MqFPLn2lAymQeAD.txt /tmp/tmplTEQNgv0UA7sFSV0Z2RL.txt
# date: Mon Nov 8 13:51:12 2010
# num seqs: 3
# dbsize(Mb): 0.000124
#
# Pre-search info for CM 1: model1.cm
#
# rnd mod alg cfg beta bit sc cut
# --- --- --- --- ----- ----------
# 1 hmm fwd loc - 3.00
# 2 cm cyk loc 1e-10 0.00
# 3 cm ins loc 1e-15 0.00
#
# CM: model1.cm
# target coord query coord
# ---------------------- ------------
# model name target name start stop start stop bit sc E-value GC%
# ------------------------------- ----------- ---------- ---------- ----- ----- -------- -------- ---
model1.cm seq_0 5 23 1 19 12.85 - 37
model1.cm seq_1 1 19 1 19 14.36 - 47
#
# Post-search info for CM 1: /tmp/tmpWmLUo5hsKH6nyib4nGMq.cm
#
# rnd mod alg cfg beta bit sc cut num hits surv fract
# --- --- --- --- ----- ---------- -------- ----------
# 1 hmm fwd loc - 3.00 2 0.4113
# 2 cm cyk loc 1e-10 0.00 2 0.4113
# 3 cm ins loc 1e-15 0.00 2 0.3065
#
# run time
# -----------
# 00:00:00"""
ALIGN_DATA = """# cmalign :: align sequences to an RNA CM
# INFERNAL 1.0.2 (October 2009)
# Copyright (C) 2009 HHMI Janelia Farm Research Campus
# Freely distributed under the GNU General Public License (GPLv3)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# command: cmalign orig_alignments/RF01057_3NPQ_chain_A_results.cm RF01057_two_seqs.fasta
# date: Thu May 1 13:00:32 2011
#
# cm name algorithm config sub bands tau
# ------------------------- --------- ------ --- ----- ------
# RF01057_3NPQ_chain_A_resu opt acc global no hmm 1e-07
#
# bit scores
# ------------------
# seq idx seq name len total struct avg prob elapsed
# ------- -------------------------- ----- -------- -------- -------- -----------
1 AABL01002928.1/2363-2445 83 55.02 2.94 0.956 00:00:00.01
2 AACV01025780.1/26051-26134 84 53.31 4.42 0.960 00:00:00.01
# STOCKHOLM 1.0
#=GF AU Infernal 1.0.2
AABL01002928.1/2363-2445 CGCGCCGAGGAGCGCUGCGACGGCCCG...UCGAGGGCCGCCAGGCUCGG
AACV01025780.1/26051-26134 CCUGCCGAGGGGCGCUGCGACCGGAUCcaaUGAGGCCCGGCCAGGCUCGG
#=GC SS_cons :::::::::<--<<<--<--<<_____...________>>->--------
#=GC RF CuuuCCGAGGAGCGCUGcAACgGgcuc...uuacggcccGCcAGGCUCGG
AABL01002928.1/2363-2445 CGGGG...ACAAucgguUUUCCAACGGCGSUCUGUUUAU
AACV01025780.1/26051-26134 UAAGGuggCUUU.....GUAACAACGGCGCCCGGCUAGA
#=GC SS_cons -----...----.....--------->>>-->:::::::
#=GC RF aaagG...uaaa.....ccuaCAACGGCGCUCAcuCaca
//
#
# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00"""
if __name__ == '__main__':
main()
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