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#!/usr/bin/env python
"""
Provides tests for StockholmParser and related classes and functions.
"""
from cogent.parse.stockholm import is_gf_line, is_gc_line, is_gs_line, \
is_gr_line, is_seq_line, is_structure_line, GfToInfo, GcToInfo, GsToInfo, \
GrToInfo, MinimalStockholmParser, StockholmFinder, \
StockholmParser, Sequence, is_empty_or_html
from cogent.util.unit_test import TestCase, main
from cogent.parse.record import RecordError
from cogent.core.info import Info
from cogent.struct.rna2d import WussStructure
from cogent.core.alignment import Alignment
from cogent.core.moltype import BYTES
__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"
Sequence = BYTES.Sequence
class StockholmParserTests(TestCase):
""" Tests componenets of the stockholm parser, in the stockholm.py file """
def setUp(self):
""" Construct some fake data for testing purposes """
self._fake_headers = []
temp = list(fake_headers.split('\n'))
for line in temp:
self._fake_headers.append(line.strip())
del temp
self._fake_gc_annotation = []
temp = list(fake_gc_annotation.split('\n'))
for line in temp:
self._fake_gc_annotation.append(line.strip())
del temp
self._fake_gs_annotation = []
temp = list(fake_gs_annotation.split('\n'))
for line in temp:
self._fake_gs_annotation.append(line.strip())
del temp
self._fake_gr_annotation = []
temp = list(fake_gr_annotation.split('\n'))
for line in temp:
self._fake_gr_annotation.append(line.strip())
del temp
self._fake_record_no_headers =\
list(fake_record_no_headers.split('\n'))
self._fake_record_no_sequences =\
list(fake_record_no_sequences.split('\n'))
self._fake_record_no_structure =\
list(fake_record_no_structure.split('\n'))
self._fake_two_records =\
list(fake_two_records.split('\n'))
self._fake_record =\
list(fake_record.split('\n'))
self._fake_record_bad_header_1 =\
list(fake_record_bad_header_1.split('\n'))
self._fake_record_bad_header_2 =\
list(fake_record_bad_header_2.split('\n'))
self._fake_record_bad_sequence_1 =\
list(fake_record_bad_sequence_1.split('\n'))
self._fake_record_bad_structure_1 =\
list(fake_record_bad_structure_1.split('\n'))
self._fake_record_bad_structure_2 =\
list(fake_record_bad_structure_2.split('\n'))
self.single_family = single_family.split('\n')
def test_is_empty_or_html(self):
"""is_empty_or_html: should ignore empty and HTML line"""
line = ' '
self.assertEqual(is_empty_or_html(line), True)
line = '\n\n'
self.assertEqual(is_empty_or_html(line), True)
line = '<pre>'
self.assertEqual(is_empty_or_html(line), True)
line = '</pre>\n\n'
self.assertEqual(is_empty_or_html(line), True)
line = '\t<//\n'
self.assertEqual(is_empty_or_html(line), False)
def test_is_gf_line(self):
"""is_gf_line: functions correctly w/ various lines """
self.assertEqual(is_gf_line('#=GF'), True)
self.assertEqual(is_gf_line('#=GF AC RF00001'), True)
self.assertEqual(is_gf_line('#=GF CC until it is\
required for transcription. '), True)
self.assertEqual(is_gf_line(''), False)
self.assertEqual(is_gf_line('X07545.1/505-619 '), False)
self.assertEqual(is_gf_line('#=G'), False)
self.assertEqual(is_gf_line('=GF'), False)
self.assertEqual(is_gf_line('#=GC SS_cons'), False)
def test_is_gc_line(self):
"""is_gc_line: functions correctly w/ various lines """
self.assertEqual(is_gc_line('#=GC'), True)
self.assertEqual(is_gc_line('#=GC SS_cons'), True)
self.assertEqual(is_gc_line('#=GC RF'), True)
self.assertEqual(is_gc_line(''), False)
self.assertEqual(is_gc_line('X07545.1/505-619 '), False)
self.assertEqual(is_gc_line('#=G'), False)
self.assertEqual(is_gc_line('=GF'), False)
self.assertEqual(is_gc_line('#=GR SS'), False)
def test_is_gs_line(self):
"""is_gs_line: functions correctly w/ various lines """
self.assertEqual(is_gs_line('#=GS'), True)
self.assertEqual(is_gs_line('#=GS Seq1 AC'), True)
self.assertEqual(is_gs_line('#=GS Seq1 DE'), True)
self.assertEqual(is_gs_line(''), False)
self.assertEqual(is_gs_line('X07545.1/505-619 '), False)
self.assertEqual(is_gs_line('#=G'), False)
self.assertEqual(is_gs_line('=GF'), False)
self.assertEqual(is_gs_line('#=GC SS_cons'), False)
def test_is_gr_line(self):
"""is_gr_line: functions correctly w/ various lines """
self.assertEqual(is_gr_line('#=GR'), True)
self.assertEqual(is_gr_line('#=GR SS ..<<..>>..'), True)
self.assertEqual(is_gr_line('#=GR RF cGGacG'), True)
self.assertEqual(is_gr_line(''), False)
self.assertEqual(is_gr_line('X07545.1/505-619 '), False)
self.assertEqual(is_gr_line('#=G'), False)
self.assertEqual(is_gr_line('=GF'), False)
self.assertEqual(is_gr_line('#=GC SS_cons'), False)
def test_is_seq_line(self):
"""is_seq_line: functions correctly w/ various lines """
s = 'X07545.1/505-619 .\
.ACCCGGC.CAUA...GUGGCCG.GGCAA.CAC.CCGG.U.C..UCGUU'
assert is_seq_line('s')
assert is_seq_line('X07545.1/505-619')
assert is_seq_line('M21086.1/8-123')
assert not is_seq_line('')
assert not is_seq_line('#GF=')
assert not is_seq_line('//blah')
def test_is_structure_line(self):
"""is_structure_line: functions correctly w/ various lines """
s = '#=GC SS_cons\
<<<<<<<<<........<<.<<<<.<...<.<...<<<<.<.<.......'
self.assertEqual(is_structure_line(s), True)
self.assertEqual(is_structure_line('#=GC SS_cons'), False)
self.assertEqual(is_structure_line('#=GC SS_cons2'), False)
self.assertEqual(is_structure_line('#=GC SS_cons '), True)
self.assertEqual(is_structure_line(''), False)
self.assertEqual(is_structure_line(' '), False)
self.assertEqual(is_structure_line('#=GF AC RF00001'), False)
self.assertEqual(is_structure_line('X07545.1/505-619'), False)
self.assertEqual(is_structure_line('=GC SS_cons'), False)
self.assertEqual(is_structure_line('#=GC'), False)
self.assertEqual(is_structure_line('#=GC RF'), False)
def test_GfToInfo(self):
"""GfToInfo: correctly builds info object from header information"""
info = GfToInfo(self._fake_headers)
self.assertEqual(info['AccessionNumber'], 'RF00001')
self.assertEqual(info['Identification'], '5S_rRNA')
self.assertEqual(info['Comment'], 'This is a short comment')
self.assertEqual(info['Author'], 'Griffiths-Jones SR')
self.assertEqual(info['Sequences'], '606')
self.assertEqual(info['DatabaseReference'],\
['URL; http://oberon.fvms.ugent.be:8080/rRNA/ssu/index.html;',\
'URL; http://rdp.cme.msu.edu/html/;'])
self.assertEqual(info['PK'],'not real')
def test_GfToInfo_invalid_data(self):
"""GfToInfo: correctly raises error when necessary """
invalid_headers = [['#=GF ACRF00001'],['#=GFACRF00001']]
for h in invalid_headers:
self.assertRaises(RecordError, GfToInfo, h)
def test_GcToInfo(self):
"""GcToInfo: correctly builds info object from header information"""
info = GcToInfo(self._fake_gc_annotation)
self.assertEqual(info['ConsensusSecondaryStructure'], \
'..........<<<<<<<<<<.....>>>>>>>>>>..')
self.assertEqual(info['ReferenceAnnotation'], \
'xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx')
def test_GcToInfo_invalid_data(self):
"""GcToInfo: correctly raises error when necessary """
invalid_headers = [['#=GCSS_cons ..<<..>>..'],['#=GCSAxxxxxxx']]
for h in invalid_headers:
self.assertRaises(RecordError, GcToInfo, h)
def test_GsToInfo(self):
"""GsToInfo: correctly builds info object from header information"""
info = GsToInfo(self._fake_gs_annotation)
self.assertEqual(info['BasePair'], \
{'1N77_C':['0 70 cWW CC','1 69 cWW CC','2 68 cWW CC',\
'3 67 cWW CC']})
def test_GsToInfo_invalid_data(self):
"""GsToInfo: correctly raises error when necessary """
invalid_headers = [['#=GSBPS 0 10 cwW CC'],['#=GSACRF00001']]
for h in invalid_headers:
self.assertRaises(RecordError, GsToInfo, h)
def test_GrToInfo(self):
"""GrToInfo: correctly builds info object from header information"""
info = GrToInfo(self._fake_gr_annotation)
self.assertEqual(info['SecondaryStructure'], \
{'1N77_C':'..........<<<<<<<<<<.....>>>>>>>>>>..'})
self.assertEqual(info['ReferenceAnnotation'], \
{'1N77_C':'xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx'})
def test_GrToInfo_invalid_data(self):
"""GrToInfo: correctly raises error when necessary """
invalid_headers = [['#=GRSS ..<<..>>..'],['#=GRSAxxxxxx']]
for h in invalid_headers:
self.assertRaises(RecordError, GrToInfo, h)
def test_StockholmStockholmParser_strict_missing_fields(self):
"""MinimalStockholmParser: toggle strict functions w/ missing fields"""
# strict = True
self.assertRaises(RecordError,list,\
MinimalStockholmParser(self._fake_record_no_sequences))
# strict = False
# no header shouldn't be a problem
headers, aln, struct = \
list(MinimalStockholmParser(self._fake_record_no_headers,\
strict=False))[0]
self.assertEqual((headers,aln.todict(),str(struct)), \
({'GS':[],'GF':[],'GR':[],\
'GC':['#=GC SS_cons ............>>>']},\
{'Z11765.1/1-89':'GGUC'},'............>>>'))
# should get empty on missing sequence or missing structure
self.assertEqual(list(MinimalStockholmParser(\
self._fake_record_no_sequences,\
strict=False)), [])
def test_MinimalStockholmParser_strict_invalid_sequence(self):
"""MinimalStockholmParser: toggle strict functions w/ invalid seq
"""
#strict = True
self.assertRaises(RecordError,list,\
MinimalStockholmParser(self._fake_record_bad_sequence_1))
# strict = False
# you expect to get back as much information as possible, also
# half records or sequences
result = MinimalStockholmParser(\
self._fake_record_bad_sequence_1,strict=False)
self.assertEqual(len(list(MinimalStockholmParser(\
self._fake_record_bad_sequence_1,strict=False))[0][1].NamedSeqs), 3)
def test_StockholmParser_strict_invalid_structure(self):
"""StockholmParser: toggle strict functions w/ invalid structure
"""
#strict = True
self.assertRaises(RecordError,list,\
StockholmParser(self._fake_record_bad_structure_1))
# strict = False
self.assertEqual(list(MinimalStockholmParser(\
self._fake_record_bad_structure_1,strict=False))[0][2],None)
def test_MinimalStockholmParser_w_valid_data(self):
"""MinimalStockholmParser: integrity of output """
# Some ugly constructions here, but this is what the output of
# parsing fake_two_records should be
headers = ['#=GF AC RF00014','#=GF AU Mifsud W']
sequences =\
{'U17136.1/898-984':\
''.join(['AACACAUCAGAUUUCCUGGUGUAACGAAUUUUUUAAGUGCUUCUUGCUUA',\
'AGCAAGUUUCAUCCCGACCCCCUCAGGGUCGGGAUUU']),\
'M15749.1/155-239':\
''.join(['AACGCAUCGGAUUUCCCGGUGUAACGAA-UUUUCAAGUGCUUCUUGCAUU',\
'AGCAAGUUUGAUCCCGACUCCUG-CGAGUCGGGAUUU']),\
'AF090431.1/222-139':\
''.join(['CUCACAUCAGAUUUCCUGGUGUAACGAA-UUUUCAAGUGCUUCUUGCAUA',\
'AGCAAGUUUGAUCCCGACCCGU--AGGGCCGGGAUUU'])}
structure = WussStructure(''.join(\
['...<<<<<<<.....>>>>>>>....................<<<<<...',\
'.>>>>>....<<<<<<<<<<.....>>>>>>>>>>..']))
data = []
for r in MinimalStockholmParser(self._fake_two_records, strict=False):
data.append(r)
self.assertEqual(\
(data[0][0]['GF'],data[0][1].todict(),\
str(data[0][2])),(headers,sequences,structure))
assert isinstance(data[0][1],Alignment)
# This line tests that invalid entries are ignored when strict=False
# Note, there are two records in self._fake_two_records, but 2nd is
# invalid
self.assertEqual(len(data),1)
def test_StockholmFinder(self):
"""StockholmFinder: integrity of output """
fake_record = ['a','//','b','b','//']
num_records = 0
data = []
for r in StockholmFinder(fake_record):
data.append(r)
num_records += 1
self.assertEqual(num_records, 2)
self.assertEqual(data[0], ['a','//'])
self.assertEqual(data[1], ['b','b','//'])
def test_StockholmParser(self):
"""StockholmParser: integrity of output """
expected_sequences =\
[''.join(['AACACAUCAGAUUUCCUGGUGUAACGAAUUUUUUAAGUGCUUCUUGCUUA',\
'AGCAAGUUUCAUCCCGACCCCCUCAGGGUCGGGAUUU']),\
''.join(['AACGCAUCGGAUUUCCCGGUGUAACGAA-UUUUCAAGUGCUUCUUGCAUU',\
'AGCAAGUUUGAUCCCGACUCCUG-CGAGUCGGGAUUU']),\
''.join(['CUCACAUCAGAUUUCCUGGUGUAACGAA-UUUUCAAGUGCUUCUUGCAUA',\
'AGCAAGUUUGAUCCCGACCCGU--AGGGCCGGGAUUU'])]
expected_structure = ''.join(\
['...<<<<<<<.....>>>>>>>....................<<<<<...',\
'.>>>>>....<<<<<<<<<<.....>>>>>>>>>>..'])
for r in StockholmParser(self._fake_record):
headers = r.Info
sequences = r
structure = r.Info['Struct']
self.assertEqual(headers['GF']['AccessionNumber'], 'RF00014')
self.assertEqual(headers['GF']['Author'], 'Mifsud W')
self.assertEqualItems(sequences.values(), expected_sequences)
assert isinstance(sequences, Alignment)
self.assertEqual(structure, expected_structure)
assert isinstance(structure,WussStructure)
def test_StockholmParser_strict_missing_fields(self):
"""StockholmParser: toggle strict functions correctly """
# strict = True
self.assertRaises(RecordError,list,\
StockholmParser(self._fake_record_no_headers))
# strict = False
self.assertEqual(list(StockholmParser(self._fake_record_no_headers,\
strict=False)), [])
self.assertEqual(list(StockholmParser(self._fake_record_no_sequences,\
strict=False)), [])
def test_StockholmParser_strict_invalid_headers(self):
"""StockholmParser: functions when toggling strict record w/ bad header
"""
self.assertRaises(RecordError,list,\
StockholmParser(self._fake_record_bad_header_1))
self.assertRaises(RecordError,list,\
StockholmParser(self._fake_record_bad_header_2))
# strict = False
x = list(StockholmParser(self._fake_record_bad_header_1, strict=False))
obs = list(StockholmParser(self._fake_record_bad_header_1,\
strict=False))[0].Info.GF.keys()
self.assertEqual(len(obs),1)
obs = list(StockholmParser(self._fake_record_bad_header_2,\
strict=False))[0].Info.GF.keys()
self.assertEqual(len(obs),1)
def test_StockholmParser_strict_invalid_sequences(self):
"""StockholmParser: functions when toggling strict w/ record w/ bad seq
"""
self.assertRaises(RecordError,list,
MinimalStockholmParser(self._fake_record_bad_sequence_1))
# strict = False
# in 'False' mode you expect to get back as much as possible, also
# parts of sequences
self.assertEqual(len(list(StockholmParser(\
self._fake_record_bad_sequence_1,\
strict=False))[0].NamedSeqs), 3)
def test_StockholmParser_strict_invalid_structure(self):
"""StockholmParser: functions when toggling strict record w/ bad struct
"""
# strict
self.assertRaises(RecordError,list,\
StockholmParser(self._fake_record_bad_structure_2))
#not strict
self.assertEqual(list(StockholmParser(\
self._fake_record_bad_structure_2,\
strict=False)),[])
def test_StockholmParser_single_family(self):
"""StockholmParser: should work on a family in stockholm format"""
exp_header = {}
exp_aln = {'K02120.1/628-682':\
'AUGGGAAAUUCCCCCUCCUAUAACCCCCCCGCUGGUAUCUCCCCCUCAGACUGGC',\
'D00647.1/629-683':\
'AUGGGAAACUCCCCCUCCUAUAACCCCCCCGCUGGCAUCUCCCCCUCAGACUGGC'}
exp_struct = '<<<<<<.........>>>>>>.........<<<<<<.............>>>>>>'
aln = list(StockholmParser(self.single_family))[0]
h = aln.Info['GF']
a = aln
s = aln.Info['Struct']
self.assertEqual(h,exp_header)
self.assertEqual(a,exp_aln)
self.assertEqual(s,exp_struct)
# This is an altered version of some header info from Rfam.seed modified to
# incorporate different cases for testing
fake_headers = """#=GF AC RF00001
#=GF AU Griffiths-Jones SR
#=GF ID 5S_rRNA
#=GF RT 5S Ribosomal RNA Database.
#=GF DR URL; http://oberon.fvms.ugent.be:8080/rRNA/ssu/index.html;
#=GF DR URL; http://rdp.cme.msu.edu/html/;
#=GF CC This is a short
#=GF CC comment
#=GF SQ 606
#=GF PK not real"""
fake_gc_annotation = """#=GC SS_cons ..........<<<<<<<<<<.....>>>>>>>>>>..
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
"""
fake_gs_annotation = """#=GS 1N77_C BP 0 70 cWW CC
#=GS 1N77_C BP 1 69 cWW CC
#=GS 1N77_C BP 2 68 cWW CC
#=GS 1N77_C BP 3 67 cWW CC
"""
fake_gr_annotation = """#=GR 1N77_C SS ..........<<<<<<<<<<.....>>>>>>>>>>..
#=GR 1N77_C RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
"""
fake_record_no_headers ="""Z11765.1/1-89 GGUC
#=GC SS_cons ............>>>
//"""
fake_record_no_sequences ="""#=GF AC RF00006
#=GC SS_cons ............>
//"""
fake_record_no_structure ="""#=GF AC RF00006
Z11765.1/1-89 GGUCAGC
//"""
fake_two_records ="""# STOCKHOLM 1.0
#=GF AC RF00014
#=GF AU Mifsud W
U17136.1/898-984 AACACAUCAGAUUUCCUGGUGUAACGAAUUUUUUAAGUGCUUCUUGCUUA
M15749.1/155-239 AACGCAUCGGAUUUCCCGGUGUAACGAA.UUUUCAAGUGCUUCUUGCAUU
AF090431.1/222-139 CUCACAUCAGAUUUCCUGGUGUAACGAA.UUUUCAAGUGCUUCUUGCAUA
#=GC SS_cons ...<<<<<<<.....>>>>>>>....................<<<<<...
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
U17136.1/898-984 AGCAAGUUUCAUCCCGACCCCCUCAGGGUCGGGAUUU
M15749.1/155-239 AGCAAGUUUGAUCCCGACUCCUG.CGAGUCGGGAUUU
AF090431.1/222-139 AGCAAGUUUGAUCCCGACCCGU..AGGGCCGGGAUUU
#=GC SS_cons .>>>>>....<<<<<<<<<<.....>>>>>>>>>>..
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
//
#=GF AC RF00015
//"""
fake_record ="""# STOCKHOLM 1.0
#=GF AC RF00014
#=GF AU Mifsud W
U17136.1/898-984 AACACAUCAGAUUUCCUGGUGUAACGAAUUUUUUAAGUGCUUCUUGCUUA
M15749.1/155-239 AACGCAUCGGAUUUCCCGGUGUAACGAA.UUUUCAAGUGCUUCUUGCAUU
AF090431.1/222-139 CUCACAUCAGAUUUCCUGGUGUAACGAA.UUUUCAAGUGCUUCUUGCAUA
#=GC SS_cons ...<<<<<<<.....>>>>>>>....................<<<<<...
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
U17136.1/898-984 AGCAAGUUUCAUCCCGACCCCCUCAGGGUCGGGAUUU
M15749.1/155-239 AGCAAGUUUGAUCCCGACUCCUG.CGAGUCGGGAUUU
AF090431.1/222-139 AGCAAGUUUGAUCCCGACCCGU..AGGGCCGGGAUUU
#=GC SS_cons .>>>>>....<<<<<<<<<<.....>>>>>>>>>>..
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
//"""
fake_record_bad_header_1 ="""# STOCKHOLM 1.0
#=GF AC RF00014
#=GF AUMifsudW
U17136.1/898-984 AACACAUCAGAUUUCCUGGUGUAACGAAUUUUUUAAGUGCUUCUUGCUUA
M15749.1/155-239 AACGCAUCGGAUUUCCCGGUGUAACGAA.UUUUCAAGUGCUUCUUGCAUU
AF090431.1/222-139 CUCACAUCAGAUUUCCUGGUGUAACGAA.UUUUCAAGUGCUUCUUGCAUA
#=GC SS_cons ...<<<<<<<.....>>>>>>>....................<<<<<...
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
U17136.1/898-984 AGCAAGUUUCAUCCCGACCCCCUCAGGGUCGGGAUUU
M15749.1/155-239 AGCAAGUUUGAUCCCGACUCCUG.CGAGUCGGGAUUU
AF090431.1/222-139 AGCAAGUUUGAUCCCGACCCGU..AGGGCCGGGAUUU
#=GC SS_cons .>>>>>....<<<<<<<<<<.....>>>>>>>>>>..
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
//"""
fake_record_bad_header_2 ="""# STOCKHOLM 1.0
#=GF AC RF00014
#=GFAUMifsud W
U17136.1/898-984 AACACAUCAGAUUUCCUGGUGUAACGAAUUUUUUAAGUGCUUCUUGCUUA
M15749.1/155-239 AACGCAUCGGAUUUCCCGGUGUAACGAA.UUUUCAAGUGCUUCUUGCAUU
AF090431.1/222-139 CUCACAUCAGAUUUCCUGGUGUAACGAA.UUUUCAAGUGCUUCUUGCAUA
#=GC SS_cons ...<<<<<<<.....>>>>>>>....................<<<<<...
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
U17136.1/898-984 AGCAAGUUUCAUCCCGACCCCCUCAGGGUCGGGAUUU
M15749.1/155-239 AGCAAGUUUGAUCCCGACUCCUG.CGAGUCGGGAUUU
AF090431.1/222-139 AGCAAGUUUGAUCCCGACCCGU..AGGGCCGGGAUUU
#=GC SS_cons .>>>>>....<<<<<<<<<<.....>>>>>>>>>>..
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
//"""
fake_record_bad_sequence_1 ="""# STOCKHOLM 1.0
#=GF AC RF00014
#=GF AU Mifsud W
U17136.1/898-984AACACAUCAGAUUUCCUGGUGUAACGAAUUUUUUAAGUGCUUCUUGCUUA
M15749.1/155-239 AACGCAUCGGAUUUCCCGGUGUAACGAA.UUUUCAAGUGCUUCUUGCAUU
AF090431.1/222-139 CUCACAUCAGAUUUCCUGGUGUAACGAA.UUUUCAAGUGCUUCUUGCAUA
#=GC SS_cons ...<<<<<<<.....>>>>>>>....................<<<<<...
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
U17136.1/898-984 AGCAAGUUUCAUCCCGACCCCCUCAGGGUCGGGAUUU
M15749.1/155-239 AGCAAGUUUGAUCCCGACUCCUG.CGAGUCGGGAUUU
AF090431.1/222-139 AGCAAGUUUGAUCCCGACCCGU..AGGGCCGGGAUUU
#=GC SS_cons .>>>>>....<<<<<<<<<<.....>>>>>>>>>>..
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
//"""
fake_record_bad_structure_1 ="""# STOCKHOLM 1.0
#=GF AC RF00014
#=GF AU Mifsud W
U17136.1/898-984 AACACAUCAGAUUUCCUGGUGUAACGAAUUUUUUAAGUGCUUCUUGCUUA
M15749.1/155-239 AACGCAUCGGAUUUCCCGGUGUAACGAA.UUUUCAAGUGCUUCUUGCAUU
AF090431.1/222-139 CUCACAUCAGAUUUCCUGGUGUAACGAA.UUUUCAAGUGCUUCUUGCAUA
#=GC SS_cons...<<<<<<<.....>>>>>>>....................<<<<<...
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
U17136.1/898-984 AGCAAGUUUCAUCCCGACCCCCUCAGGGUCGGGAUUU
M15749.1/155-239 AGCAAGUUUGAUCCCGACUCCUG.CGAGUCGGGAUUU
AF090431.1/222-139 AGCAAGUUUGAUCCCGACCCGU..AGGGCCGGGAUUU
#=GC SS_cons .>>>>>....<<<<<<<<<<.....>>>>>>>>>>..
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
//"""
fake_record_bad_structure_2 ="""# STOCKHOLM 1.0
#=GF AC RF00014
#=GF AU Mifsud W
U17136.1/898-984 AACACAUCAGAUUUCCUGGUGUAACGAAUUUUUUAAGUGCUUCUUGCUUA
M15749.1/155-239 AACGCAUCGGAUUUCCCGGUGUAACGAA.UUUUCAAGUGCUUCUUGCAUU
AF090431.1/222-139 CUCACAUCAGAUUUCCUGGUGUAACGAA.UUUUCAAGUGCUUCUUGCAUA
#=GC SS_cons ...<<<<<<<.....>>>>>>>....................<<<<<!!!
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
U17136.1/898-984 AGCAAGUUUCAUCCCGACCCCCUCAGGGUCGGGAUUU
M15749.1/155-239 AGCAAGUUUGAUCCCGACUCCUG.CGAGUCGGGAUUU
AF090431.1/222-139 AGCAAGUUUGAUCCCGACCCGU..AGGGCCGGGAUUU
#=GC SS_cons .>>>>>....<<<<<<<<<<.....>>>>>>>>>>..
#=GC RF xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
//"""
single_family=\
"""K02120.1/628-682 AUGGGAAAUUCCCCCUCCUAUAACCCCCCCGCUGGUAUCUCCCCCUCAGA
D00647.1/629-683 AUGGGAAACUCCCCCUCCUAUAACCCCCCCGCUGGCAUCUCCCCCUCAGA
#=GC SS_cons <<<<<<.........>>>>>>.........<<<<<<.............>
K02120.1/628-682 CUGGC
D00647.1/629-683 CUGGC
#=GC SS_cons >>>>>
//"""
# Run tests if called from the command line
if __name__ == '__main__':
main()
|
