diff --git a/core/tests/data/fasta/1ake.fas b/core/tests/data/fasta/1ake.fas
index 024c40b462b71087ab6316084af16b9fed35ed69..6e08a6c407f9c016660376c29376b7ade696d12f 100644
--- a/core/tests/data/fasta/1ake.fas
+++ b/core/tests/data/fasta/1ake.fas
@@ -1,8 +1,8 @@
> 1AKE.B
MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNG
FLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQ
-EETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTKPV---AEVRADLEKILG
+EETVRKRLVEYHQMTAPLIGYYYYSKEAEAGNTKYAKVDGTKPV---AEVRADLEKILG
> target
-------APGAGKGTQAQFIMEKYGIPQISTGGGLRAAVKS---LGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNG
FLLDGFPRTIPQADAMKEAGINVDYVLEF----ELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQ
-EETVRKRLVEYHQMTAPLLYYYYKEAEAGNTKYAKVDGTKPVAEVRADLEKILG---
+EETVRKRLVEYHQMTAPLL--YYYYKEAEAGNTKYAKVDGTKPVAEVRADLEKILG---
diff --git a/core/tests/test_pm3argparse.py b/core/tests/test_pm3argparse.py
index 9b4dff068f6e013ff4a0548b206d41b55420c613..117b32fd3a03941cc0db3f8351d51a627524e218 100644
--- a/core/tests/test_pm3argparse.py
+++ b/core/tests/test_pm3argparse.py
@@ -1,69 +1,244 @@
-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
diff --git a/extras/pre_commit/pm3_csc/filecheck/pylintrc b/extras/pre_commit/pm3_csc/filecheck/pylintrc
index 66347b07c03d811f78ebcd2f93b44d80de13dc73..b9244937e453b7f8865f36d5e7778372b66c1fd5 100644
--- a/extras/pre_commit/pm3_csc/filecheck/pylintrc
+++ b/extras/pre_commit/pm3_csc/filecheck/pylintrc
@@ -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]