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#!/usr/bin/env python
"""For use with hmmer3"""
from cogent.parse.hmmscan import MinimalTbloutParser, RichTbloutParser
from cogent.util.unit_test import TestCase, main
__author__ = "Daniel McDonald"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Daniel McDonald"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Daniel McDonald"
__email__ = "daniel.mcdonald@colorado.edu"
__status__ = "Prototype"
class hmmscanTests(TestCase):
def setUp(self):
pass
def test_MinimalTbloutParser(self):
"""MinimalTbloutParser tests"""
exp1 = ['Sulfotransfer_3','PF13469.1','NC_008340.4664','-','1.7e-14',
'43.6','0.0','3.4e-14','42.6','0.0','1.5','1','0','0','1','1',
'1','1','Sulfotransferase family']
exp2 = ['UreD', 'PF01774.12', 'NC_008340.6164', '-', '4e-62', '198.0',
'0.0', '4.9e-62', '197.7', '0.0', '1.1', '1', '0', '0', '1',
'1', '1', '1', 'UreD urease accessory protein']
exp3 = ['UreF', 'PF01730.11', 'NC_008340.6172', '-', '1.9e-51',
'162.7', '10.3', '2.8e-51', '162.1', '7.1', '1.3', '1', '0',
'0', '1', '1', '1', '1', 'UreF']
parser = MinimalTbloutParser(tblout)
self.assertEqual(parser.next(), exp1)
self.assertEqual(parser.next(), exp2)
self.assertEqual(parser.next(), exp3)
self.assertRaises(StopIteration, parser.next)
def test_RichTbloutParser(self):
"""More useful returns"""
headers = ["target name", "target accession", "query name",
"query accession","full seq E-value", "full seq score",
"full seq bias","best 1 domain E-value",
"best 1 domain score", "best 1 domain bias", "exp","reg",
"clu","ov","env","dom","rep","inc","description of target"]
types = [str,str,str,str,float,float,float,float,float,float,float,int,
int,int,int,int,int,int,str]
expbase1 = ['Sulfotransfer_3','PF13469.1','NC_008340.4664','-','1.7e-14',
'43.6','0.0','3.4e-14','42.6','0.0','1.5','1','0','0','1','1',
'1','1','Sulfotransferase family']
expbase2 = ['UreD', 'PF01774.12', 'NC_008340.6164', '-', '4e-62',
'198.0', '0.0', '4.9e-62', '197.7', '0.0', '1.1', '1', '0',
'0', '1', '1', '1', '1', 'UreD urease accessory protein']
expbase3 = ['UreF', 'PF01730.11', 'NC_008340.6172', '-', '1.9e-51',
'162.7', '10.3', '2.8e-51', '162.1', '7.1', '1.3', '1', '0',
'0', '1', '1', '1', '1', 'UreF']
exp1 = dict([(h,t(e)) for h,t,e in zip(headers,types,expbase1)])
exp2 = dict([(h,t(e)) for h,t,e in zip(headers,types,expbase2)])
exp3 = dict([(h,t(e)) for h,t,e in zip(headers,types,expbase3)])
parser = RichTbloutParser(tblout)
self.assertEqual(parser.next(), exp1)
self.assertEqual(parser.next(), exp2)
self.assertEqual(parser.next(), exp3)
self.assertRaises(StopIteration, parser.next)
tblout = """# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
Sulfotransfer_3 PF13469.1 NC_008340.4664 - 1.7e-14 43.6 0.0 3.4e-14 42.6 0.0 1.5 1 0 0 1 1 1 1 Sulfotransferase family
UreD PF01774.12 NC_008340.6164 - 4e-62 198.0 0.0 4.9e-62 197.7 0.0 1.1 1 0 0 1 1 1 1 UreD urease accessory protein
UreF PF01730.11 NC_008340.6172 - 1.9e-51 162.7 10.3 2.8e-51 162.1 7.1 1.3 1 0 0 1 1 1 1 UreF""".splitlines()
if __name__ == '__main__':
main()
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