def run_unzip(filepath, newpath=None, singleFile=False, **kwargs):
'''run unzip program as a sub process,
save to single file newpath if desired.'''
if newpath is None:
newpath = filepath[:-4] # DROP THE .zip SUFFIX
if singleFile: # concatenate all files into newpath
ifile = file(newpath, 'wb') # copy as binary file
try:
status = call_subprocess(['unzip', '-p', filepath], stdout=ifile)
finally:
ifile.close()
else: # just unzip the package as usual
status = call_subprocess(['unzip', filepath])
if status != 0:
raise OSError('unzip "%s" failed!' % filepath)
return newpath
def run_unzip(filepath, newpath=None, singleFile=False, **kwargs):
'''run unzip program as a sub process,
save to single file newpath if desired.'''
if newpath is None:
newpath = filepath[:-4] # DROP THE .zip SUFFIX
if singleFile: # concatenate all files into newpath
ifile = file(newpath, 'wb') # copy as binary file
try:
status = call_subprocess(['unzip', '-p', filepath], stdout=ifile)
finally:
ifile.close()
else: # just unzip the package as usual
status = call_subprocess(['unzip', filepath])
if status != 0:
raise OSError('unzip "%s" failed!' % filepath)
return newpath
def run_gunzip(filepath, newpath=None):
'run gunzip program as a sub process'
if newpath is None:
newpath = filepath[:-3]
ifile = open(newpath, 'w+b')
try:
if call_subprocess(['gunzip', '-c', filepath], stdout=ifile):
raise OSError('gunzip "%s" failed!' % filepath)
finally:
ifile.close()
return newpath
def run_gunzip(filepath, newpath=None):
'run gunzip program as a sub process'
if newpath is None:
newpath = filepath[:-3]
ifile = open(newpath, 'w+b')
try:
if call_subprocess(['gunzip', '-c', filepath], stdout=ifile):
raise OSError('gunzip "%s" failed!' % filepath)
finally:
ifile.close()
return newpath
def run_formatdb(self, filepath):
'ATTEMPT TO BUILD BLAST DATABASE INDEXES at filepath'
dirname = classutil.file_dirpath(filepath)
if not os.access(dirname, os.W_OK): # check if directory is writable
raise IOError('run_formatdb: directory %s is not writable!'
% dirname)
cmd = ['formatdb', '-i', self.filepath, '-n', filepath, '-o', 'T']
if self.seqDB._seqtype != PROTEIN_SEQTYPE:
cmd += ['-p', 'F'] # special flag required for nucleotide seqs
logger.info('Building index: ' + ' '.join(cmd))
if classutil.call_subprocess(cmd): # bad exit code, so command failed
raise OSError('command %s failed' % ' '.join(cmd))
self.blastReady=True
if filepath!=self.filepath:
self.blastIndexPath = filepath
def run_formatdb(self, testpath):
'ATTEMPT TO BUILD BLAST DATABASE INDEXES at testpath'
dirname = classutil.file_dirpath(testpath)
if not os.access(dirname, os.W_OK): # check if directory is writable
raise IOError('run_formatdb: directory %s is not writable!'
% dirname)
cmd = ['formatdb', '-i', self.filepath, '-n', testpath, '-o', 'T']
if self.seqDB._seqtype != PROTEIN_SEQTYPE:
cmd += ['-p', 'F'] # special flag required for nucleotide seqs
logger.info('Building index: ' + ' '.join(cmd))
if self.showFormatdbMessages:
kwargs = {}
else: # suppress formatdb messages by redirecting them
kwargs = dict(stdout=classutil.PIPE, stderr=classutil.PIPE)
if classutil.call_subprocess(cmd, **kwargs):
# bad exit code, so command failed
warn_if_whitespace(self.filepath) \
or warn_if_whitespace(testpath) # only issue one warning
raise OSError('command %s failed' % ' '.join(cmd))
self.blastReady=True
if testpath!=self.filepath:
self.blastIndexPath = testpath
