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More informative error message for bam conversion errors.

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Hopefully this will help debug this issue (https://trello.com/c/TL0IdLlG) reported by @peterjc.
This commit is contained in:
John Chilton
2015-03-23 09:35:21 -04:00
parent 75275bbcef
commit 8cb06d7fc2
1 changed files with 14 additions and 4 deletions
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test/base/twilltestcase.py
+14 -4
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@@ -2450,14 +2450,24 @@ class TwillTestCase( unittest.TestCase ):
errmsg += self.get_job_stderr( dataset.get( 'id' ), format=True )
raise AssertionError( errmsg )
def _check_command(self, command, description):
# TODO: also collect ``which samtools`` and ``samtools --version``
p = subprocess.Popen( args=command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True )
(stdout, stderr) = p.communicate()
if p.returncode:
template = description
template += " failed: (cmd=[%s], stdout=[%s], stderr=[%s])"
message = template % (command, stdout, stderr)
raise AssertionError(message)
def _bam_to_sam( self, local_name, temp_name ):
temp_local = tempfile.NamedTemporaryFile( suffix='.sam', prefix='local_bam_converted_to_sam_' )
fd, temp_temp = tempfile.mkstemp( suffix='.sam', prefix='history_bam_converted_to_sam_' )
os.close( fd )
p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % ( temp_local.name, local_name ), shell=True )
assert not p.wait(), 'Converting local (test-data) bam to sam failed'
p = subprocess.Popen( args='samtools view -h -o "%s" "%s"' % ( temp_temp, temp_name ), shell=True )
assert not p.wait(), 'Converting history bam to sam failed'
command = 'samtools view -h -o "%s" "%s"' % ( temp_local.name, local_name )
self._check_command( command, 'Converting local (test-data) bam to sam' )
command = 'samtools view -h -o "%s" "%s"' % ( temp_temp, temp_name )
self._check_command( command, 'Converting history bam to sam ' )
os.remove( temp_name )
return temp_local, temp_temp