def _set_version(self):
self.version = None
if self.debug:
print(self.name, '- checking version ...')
if not self.in_path():
if self.debug:
print(' ... not in path so cannot get version', flush=True)
return
cmd = self.exe() + ' ' + self.version_cmd
if self.debug:
print('Running this command to get version:', 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]
if self.debug:
print('__________ (begin output from ', cmd, ')___________', sep='')
print(*cmd_output, sep='\n')
print('__________ (end of output from ', cmd, ')___________', sep='')
print('Looking far a match to the regex "', self.version_regex.pattern, '" in the above output', sep='', flush=True)
for line in cmd_output:
hits = self.version_regex.search(line)
if hits:
if self.debug:
print('Match to this line:', line)
print('Got version:', hits.group(1), flush=True)
self.version = hits.group(1)
break
else:
if self.debug:
print('No match found to the regex', flush=True)
def version(self):
'''Returns version. If not in path, or in path but can't get the version, returns None'''
if not self.in_path():
return None
cmd = self.exe() + ' ' + self.version_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 = self.version_regex.search(line)
if hits:
return hits.group(1)
return None
def _set_version(self):
self.version = None
if self.debug:
print(self.name, '- checking version ...')
if not self.in_path():
if self.debug:
print(' ... not in path so cannot get version', flush=True)
return
cmd = self.exe() + ' ' + self.version_cmd
if self.debug:
print('Running this command to get version:', 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]
if self.debug:
print('__________ (begin output from ',
cmd,
')___________',
sep='')
print(*cmd_output, sep='\n')
print('__________ (end of output from ',
cmd,
')___________',
sep='')
print('Looking far a match to the regex "',
self.version_regex.pattern,
'" in the above output',
sep='',
flush=True)
for line in cmd_output:
hits = self.version_regex.search(line)
if hits:
if self.debug:
print('Match to this line:', line)
print('Got version:', hits.group(1), flush=True)
self.version = hits.group(1)
break
else:
if self.debug:
print('No match found to the regex', flush=True)
def aligned_read_to_read(read, revcomp=True, qual=None, ignore_quality=False):
'''Returns Fasta or Fastq sequence from pysam aligned read'''
if read.qual is None or ignore_quality:
if qual is None or ignore_quality:
seq = pyfastaq.sequences.Fasta(read.qname, common.decode(read.seq))
else:
seq = pyfastaq.sequences.Fastq(read.qname, common.decode(read.seq), qual * read.query_length)
else:
if qual is None:
seq = pyfastaq.sequences.Fastq(read.qname, common.decode(read.seq), common.decode(read.qual))
else:
seq = pyfastaq.sequences.Fastq(read.qname, common.decode(read.seq), qual * read.query_length)
if read.is_reverse and revcomp:
seq.revcomp()
return seq
def aligned_read_to_read(read, revcomp=True, qual=None, ignore_quality=False):
'''Returns Fasta or Fastq sequence from pysam aligned read'''
if read.qual is None or ignore_quality:
if qual is None or ignore_quality:
seq = pyfastaq.sequences.Fasta(read.qname, common.decode(read.seq))
else:
seq = pyfastaq.sequences.Fastq(read.qname, common.decode(read.seq), qual * read.query_length)
else:
if qual is None:
seq = pyfastaq.sequences.Fastq(read.qname, common.decode(read.seq), common.decode(read.qual))
else:
seq = pyfastaq.sequences.Fastq(read.qname, common.decode(read.seq), qual * read.query_length)
if read.is_reverse and revcomp:
seq.revcomp()
return seq
def version(self):
'''Returns version. If not in path, or in path but can't get the version, returns None'''
if not self.in_path():
return None
cmd = self.exe() + ' ' + self.version_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 = self.version_regex.search(line)
if hits:
return hits.group(1)
return None
