def get_version(prog, path=None, raise_error=True):
assert prog in prog_to_version_cmd
if path is None:
path = prog
if not is_in_path(path):
if raise_error:
raise Error('Error getting version of ' + path + ' - not found in path.')
else:
return 'Not_in_path', 'Not_in_path'
path = shutil.which(path)
if prog in ['sspace', 'gapfiller']:
cmd = 'perl ' + os.path.realpath(shutil.which(path))
regex = prog_to_version_cmd[prog][1]
else:
cmd, regex = prog_to_version_cmd[prog]
cmd = path + ' ' + cmd
cmd_output = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
cmd_output = common.decode(cmd_output[0]).split('\n')[:-1] + common.decode(cmd_output[1]).split('\n')[:-1]
for line in cmd_output:
hits = regex.search(line)
if hits:
return hits.group(1), path
return 'UNKNOWN ...\n I tried running this to get the version: "' + cmd + '"\n and the output didn\'t match this regular expression: "' + regex.pattern + '"', path
def _sam_to_fastq(self, s):
name = s.qname
if s.is_read1:
name += '/1'
elif s.is_read2:
name += '/2'
else:
raise Error('Read ' + name + ' must be first or second of pair according to flag. Cannot continue')
seq = pyfastaq.sequences.Fastq(name, common.decode(s.seq), common.decode(s.qual))
if s.is_reverse:
seq.revcomp()
return seq
def sam_to_fastq(sam):
'''Given a pysam alignment, returns the sequence a Fastq object.
Reverse complements as required and add suffix /1 or /2 as appropriate from the flag'''
name = sam.qname
if sam.is_read1:
name += '/1'
elif sam.is_read2:
name += '/2'
else:
raise Error('Read ' + name + ' must be first or second of pair according to flag. Cannot continue')
seq = pyfastaq.sequences.Fastq(name, common.decode(sam.seq), common.decode(sam.qual))
if sam.is_reverse:
seq.revcomp()
return seq
def _get_version(prog, path):
'''Given a program name and expected path, tries to determine its version.
Returns tuple (bool, version). First element True iff found version ok.
Second element is version string (if found), otherwise an error message'''
assert prog in prog_to_version_cmd
cmd, regex = prog_to_version_cmd[prog]
cmd = path + ' ' + cmd
cmd_output = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
cmd_output = common.decode(cmd_output[0]).split('\n')[:-1] + common.decode(cmd_output[1]).split('\n')[:-1]
for line in cmd_output:
hits = regex.search(line)
if hits:
return True, hits.group(1)
return False, 'I tried to get the version of ' + prog + ' with: "' + cmd + '" and the output didn\'t match this regular expression: "' + regex.pattern + '"'
def sam_to_fastq(sam):
'''Given a pysam alignment, returns the sequence a Fastq object.
Reverse complements as required and add suffix /1 or /2 as appropriate from the flag'''
name = sam.qname
if sam.is_read1:
name += '/1'
elif sam.is_read2:
name += '/2'
else:
raise Error(
'Read ' + name +
' must be first or second of pair according to flag. Cannot continue'
)
seq = pyfastaq.sequences.Fastq(name, common.decode(sam.seq),
common.decode(sam.qual))
if sam.is_reverse:
seq.revcomp()
return seq
def _get_version(prog, path):
'''Given a program name and expected path, tries to determine its version.
Returns tuple (bool, version). First element True iff found version ok.
Second element is version string (if found), otherwise an error message'''
assert prog in prog_to_version_cmd
cmd, regex = prog_to_version_cmd[prog]
cmd = path + ' ' + cmd
cmd_output = subprocess.Popen(cmd,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE).communicate()
cmd_output = common.decode(
cmd_output[0]).split('\n')[:-1] + common.decode(
cmd_output[1]).split('\n')[:-1]
for line in cmd_output:
hits = regex.search(line)
if hits:
return True, hits.group(1)
return False, 'I tried to get the version of ' + prog + ' with: "' + cmd + '" and the output didn\'t match this regular expression: "' + regex.pattern + '"'
