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Commit af547e54 authored by Bienchen's avatar Bienchen
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--fasta option

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core/tests/data/fasta/1ake.fas
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− 2
View file @ af547e54
> 1AKE.B
MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNG
FLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQ
EETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTKPV---AEVRADLEKILG
EETVRKRLVEYHQMTAPLIGYYYYSKEAEAGNTKYAKVDGTKPV---AEVRADLEKILG
> target
-------APGAGKGTQAQFIMEKYGIPQISTGGGLRAAVKS---LGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNG
FLLDGFPRTIPQADAMKEAGINVDYVLEF----ELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQ
EETVRKRLVEYHQMTAPLLYYYYKEAEAGNTKYAKVDGTKPVAEVRADLEKILG---
EETVRKRLVEYHQMTAPLL--YYYYKEAEAGNTKYAKVDGTKPVAEVRADLEKILG---
core/tests/test_pm3argparse.py
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View file @ af547e54
import unittest, sys
import unittest
import ost
from promod3.core import pm3argparse
#argparse writes to stdout/ stderr so we need to fetch it
class _FetchStd(object):
def __init__(self):
self.buffer = list()
def write(self, line):
self.buffer.append(line.strip())
class _FetchLog(ost.LogSink):
"""
Capturing output of the OST logger
"""
def __init__(self):
ost.LogSink.__init__(self)
self.messages = dict()
def flush(self):
pass
def LogMessage(self, message, severity):
levels = ['ERROR', 'WARNING', 'SCRIPT', 'INFO', 'VERBOSE', 'DEBUG',
'TRACE']
level = levels[severity]
if not level in self.messages.keys():
self.messages[level] = list()
self.messages[level].append(message.strip())
class PM3ArgParseTests(unittest.TestCase):
def setUp(self):
self.original_stderr = sys.stderr
self.original_stdout = sys.stdout
sys.stderr = _FetchStd()
sys.stdout = _FetchStd()
self.log = _FetchLog()
ost.PushLogSink(self.log)
ost.PushVerbosityLevel(2)
def tearDown(self):
sys.stderr = self.original_stderr
sys.stdout = self.original_stdout
ost.PopVerbosityLevel()
ost.PopLogSink()
def testUnrecognisedArguments(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
with self.assertRaises(SystemExit) as ec:
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['-x'])
self.assertEqual(ec.exception.code, 2)
self.assertEqual(sys.stderr.buffer, ['usage: test_pm3argparse.py [-h]',
'test_pm3argparse.py: error: '+
'unrecognized arguments: -x'])
self.assertEqual(ecd.exception.code, 2)
self.assertEqual(self.log.messages['ERROR'],
['usage: test_pm3argparse.py [-h]',
'test_pm3argparse.py: error: unrecognized '+
'arguments: -x'])
def testActionSwitch(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
with self.assertRaises(SystemExit) as ec:
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['--help'])
self.assertEqual(ec.exception.code, 0)
self.assertEqual(sys.stdout.buffer, ['usage: test_pm3argparse.py '+
'[-h]\n\noptional arguments:\n '+
'-h, --help show this help '+
'message and exit'])
self.assertEqual(ecd.exception.code, 0)
self.assertEqual(self.log.messages['SCRIPT'],
['usage: test_pm3argparse.py [-h]\n\noptional '+
'arguments:\n -h, --help show this help message '+
'and exit'])
sys.stdout.buffer = list()
self.log.messages = dict()
parser = pm3argparse.PM3ArgumentParser(action=True)
with self.assertRaises(SystemExit) as ec:
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['--help'])
self.assertEqual(ec.exception.code, 0)
self.assertEqual(sys.stdout.buffer, ['usage: t_pm3argparse.py '+
'[-h]\n\noptional arguments:\n '+
'-h, --help show this help '+
'message and exit'])
self.assertEqual(ecd.exception.code, 0)
self.assertEqual(self.log.messages['SCRIPT'],
['usage: t_pm3argparse.py [-h]\n\noptional '+
'arguments:\n -h, --help show this help message '+
'and exit'])
def testDescription(self):
parser = pm3argparse.PM3ArgumentParser(action=False,
description='This is a test.')
with self.assertRaises(SystemExit) as ec:
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['--help'])
self.assertEqual(ec.exception.code, 0)
self.assertEqual(sys.stdout.buffer, ['usage: test_pm3argparse.py '+
'[-h]\n\nThis is a '+
'test.\n\noptional arguments:\n '+
'-h, --help show this help '+
'message and exit'])
self.assertEqual(ecd.exception.code, 0)
self.assertEqual(self.log.messages['SCRIPT'],
['usage: test_pm3argparse.py [-h]\n\nThis is a '+
'test.\n\noptional arguments:\n -h, --help show '+
'this help message and exit'])
def testAddAlignemntNoTrgPfx(self):
# checking that we fail on missing 'trg:' prefix for arguments of
# --fasta
parser = pm3argparse.PM3ArgumentParser(action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['--fasta', 'foo', 'bar'])
self.assertEqual(ecd.exception.code, 11)
self.assertEqual(self.log.messages['ERROR'][0],
"'--fasta' requires one "+
"argument prefixed with 'trg:' marking the target "+
"sequence name")
def testAddAlignemntEmptyTrgPfx(self):
# checking that we fail on empty 'trg:' prefix for arguments of
# --fasta
parser = pm3argparse.PM3ArgumentParser(action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['--fasta', 'trg:', 'bar'])
self.assertEqual(ecd.exception.code, 14)
self.assertEqual(self.log.messages['ERROR'][0], "'--fasta' requires "+
"argument 'trg:' defining the target sequence name, "+
"empty one found: 'trg: bar'")
def testAddAlignemntSwapTrgPfx(self):
# checking that we fail on empty 'trg:' prefix for arguments of
# --fasta
parser = pm3argparse.PM3ArgumentParser(action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['--fasta', 'bar', 'trg:'])
self.assertEqual(ecd.exception.code, 14)
self.assertEqual(self.log.messages['ERROR'][0], "'--fasta' requires "+
"argument 'trg:' defining the target sequence name, "+
"empty one found: 'bar trg:'")
def testAddAlignmentNoFile(self):
# check that we throw an error if a non-exisiting file is given
parser = pm3argparse.PM3ArgumentParser(action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['--fasta', 'trg:foo', 'notexistingfile.fas'])
self.assertEqual(ecd.exception.code, 12)
self.assertEqual(self.log.messages['ERROR'][0],
"Alignment file does not exist: notexistingfile.fas")
def testAddAlignmentEmpty(self):
# we want to fail if we get an empty FastA file
parser = pm3argparse.PM3ArgumentParser(action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['--fasta', 'trg:foo', 'data/fasta/alignment.fas'])
self.assertEqual(ecd.exception.code, 15)
self.assertEqual(self.log.messages['ERROR'][0],
"'--fasta' refers to an empty file or its in the "+
"wrong format: data/fasta/alignment.fas")
def testAddAlignmentToMany(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['--fasta', 'trg:target', 'data/fasta/1ake_3.fas'])
self.assertEqual(ecd.exception.code, 16)
self.assertEqual(self.log.messages['ERROR'][0], "'--fasta trg:target "+
"data/fasta/1ake_3.fas' points to an alignment with "+
"more than 2 sequences.")
def testAddAlignmentMissingTargetName(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['--fasta', 'trg:trg', 'data/fasta/1ake.fas'])
self.assertEqual(ecd.exception.code, 17)
self.assertEqual(self.log.messages['ERROR'][0], "'--fasta trg:trg "+
"data/fasta/1ake.fas' does not define a target name "+
"found in the alignment.")
def testAddAlignmentDifferentSeqLens(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
parser.AddAlignment()
parser.AssembleParser()
with self.assertRaises(SystemExit) as ecd:
parser.Parse(['--fasta', 'trg:target', 'data/fasta/1ake_nel.fas'])
self.assertEqual(ecd.exception.code, 18)
self.assertEqual(self.log.messages['ERROR'][0], "'--fasta trg:target "+
"data/fasta/1ake_nel.fas': sequences in the "+
"alignment have different length.")
def testAddAlignmentGzipIn(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
parser.AddAlignment()
parser.AssembleParser()
opts = parser.Parse(['--fasta', 'trg:target',
'data/fasta/1ake.fas.gz', '--fasta', 'trg:target',
'data/fasta/1ake.fas'])
self.assertEqual(str(opts.alignments[0]), 'target APGAGKGTQAQFIMEKYG'+
'IPQISTGGGLRAAVKS---LGKQAKDIMDAGKLVTDELVIALVKERIAQED'+
'CRN\n1AKE.B APGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSEL'+
'GKQAKDIMDAGKLVTDELVIALVKERIAQEDCRN\n\ntarget GFLLD'+
'GFPRTIPQADAMKEAGINVDYVLEF----ELIVDRIVGRRVHAPSGRVYHV'+
'KFNPPKVEGKDDVTGE\n1AKE.B GFLLDGFPRTIPQADAMKEAGINVD'+
'YVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGE\n\n'+
'target ELTTRKDDQEETVRKRLVEYHQMTAPLLYYYYKEAEAGNTKYA'+
'KVDGTKPVAEVRADLEKILG\n1AKE.B ELTTRKDDQEETVRKRLVEYH'+
'QMTAPLIGYYSKEAEAGNTKYAKVDGTKPV---AEVRADLEK\n')
self.assertEqual(opts.alignments[0].GetSequence(1).offset, 7)
self.assertEqual(str(opts.alignments[1]), 'target APGAGKGTQAQFIMEKYG'+
'IPQISTGGGLRAAVKS---LGKQAKDIMDAGKLVTDELVIALVKERIAQED'+
'CRN\n1AKE.B APGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSEL'+
'GKQAKDIMDAGKLVTDELVIALVKERIAQEDCRN\n\ntarget GFLLD'+
'GFPRTIPQADAMKEAGINVDYVLEF----ELIVDRIVGRRVHAPSGRVYHV'+
'KFNPPKVEGKDDVTGE\n1AKE.B GFLLDGFPRTIPQADAMKEAGINVD'+
'YVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGE\n\n'+
'target ELTTRKDDQEETVRKRLVEYHQMTAPLL--YYYYKEAEAGNTK'+
'YAKVDGTKPVAEVRADLEKILG\n1AKE.B ELTTRKDDQEETVRKRLVE'+
'YHQMTAPLIGYYYYSKEAEAGNTKYAKVDGTKPV---AEVRADLEK\n')
def testAddAlignmentSwitchSeqs(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
parser.AddAlignment()
parser.AssembleParser()
opts = parser.Parse(['--fasta', 'trg:target',
'data/fasta/1ake.fas'])
self.assertEqual(str(opts.alignments[0].GetSequence(0)),
'APGAGKGTQAQFIMEKYGIPQISTGGGLRAAVKS---LGKQAKDIMDAGK'+
'LVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVL'+
'EF----ELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRK'+
'DDQEETVRKRLVEYHQMTAPLL--YYYYKEAEAGNTKYAKVDGTKPVAEV'+
'RADLEKILG')
parser = pm3argparse.PM3ArgumentParser(action=False)
parser.AddAlignment()
parser.AssembleParser()
opts = parser.Parse(['--fasta', 'trg:target',
'data/fasta/1ake_sw.fas'])
self.assertEqual(str(opts.alignments[0].GetSequence(0)),
'APGAGKGTQAQFIMEKYGIPQISTGGGLRAAVKS---LGKQAKDIMDAGK'+
'LVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVL'+
'EF----ELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRK'+
'DDQEETVRKRLVEYHQMTAPLL--YYYYKEAEAGNTKYAKVDGTKPVAEV'+
'RADLEKILG')
def testAddAlignment(self):
parser = pm3argparse.PM3ArgumentParser(action=False)
parser.AddAlignment()
parser.AssembleParser()
opts = parser.Parse(['--fasta', 'trg:target',
'data/fasta/1ake.fas'])
self.assertEqual(len(opts.alignments), 1)
self.assertEqual(opts.alignments[0].GetLength(), 209)
self.assertEqual(opts.alignments[0].GetSequenceOffset(0), 0)
self.assertEqual(opts.alignments[0].GetSequenceOffset(1), 7)
self.assertEqual(opts.alignments[0].GetSequence(0).gapless_string,
'APGAGKGTQAQFIMEKYGIPQISTGGGLRAAVKSLGKQAKDIMDAGKLVT'+
'DELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFE'+
'LIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETV'+
'RKRLVEYHQMTAPLLYYYYKEAEAGNTKYAKVDGTKPVAEVRADLEKILG')
self.assertEqual(opts.alignments[0].GetSequence(0).name, 'target')
self.assertEqual(opts.alignments[0].GetSequence(1).name, '1AKE.B')
self.assertEqual(opts.aln_sources[0], 'data/fasta/1ake.fas')
if __name__ == "__main__":
from ost import testutils
......
extras/pre_commit/pm3_csc/filecheck/pylintrc
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− 1
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......@@ -290,7 +290,7 @@ max-attributes=7
min-public-methods=2
# Maximum number of public methods for a class (see R0904).
max-public-methods=20
max-public-methods=21
[IMPORTS]
......
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