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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
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.4.1"
__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
Target_1 1 10 1 10 25.25 - 50
Target_2 3 13 1 10 14.2 - 49
# Post search summary
"""
self.basic_res = [['Target_1', 1, 10, 1, 10, 25.25, '-', 50],\
['Target_2', 3, 13, 1, 10, 14.2, '-', 49]]
self.search_res = [['seq_a', 5, 23, 1, 19, 12.85, '-', 37],\
['seq_b', 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)
SEARCH_DATA = """# command: cmsearch --tabfile aln1_seqs2_searchres.txt aln1.cm seqs2.fasta
# date: Tue Oct 7 17:11:59 2008
# num seqs: 6
# dbsize(Mb): 0.000230
#
# Pre-search info for CM 1: aln1-1
#
# rnd mod alg cfg beta bit sc cut
# --- --- --- --- ----- ----------
# 1 hmm fwd loc - 3.00
# 2 cm cyk loc 1e-07 0.00
# 3 cm ins loc 1e-15 0.00
#
# CM: aln1-1
# target coord query coord
# ---------------------- ------------
# target name start stop start stop bit sc E-value GC%
# ----------- ---------- ---------- ----- ----- -------- -------- ---
seq_a 5 23 1 19 12.85 - 37
seq_b 1 19 1 19 14.36 - 47
#
# Post-search info for CM 1: aln1-1
#
# rnd mod alg cfg beta bit sc cut num hits surv fract
# --- --- --- --- ----- ---------- -------- ----------
# 1 hmm fwd loc - 3.00 2 0.2217
# 2 cm cyk loc 1e-07 0.00 2 0.2217
# 3 cm ins loc 1e-15 0.00 2 0.1652
#
# run time
# -----------
# 00:00:00"""
if __name__ == '__main__':
main()
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