dumpOut()
sys.exit(1)
def sizeof_fmt(num, suffix='B'):
for unit in ['','K','M','G','T','P','E','Z']:
if abs(num) < 1024.0:
return "%3.1f%s%s" % (num, unit, suffix)
num /= 1024.0
return "%.1f%s%s" % (num, 'Yi', suffix)
InDir = os.getcwd()
if len(Args): InDir = Args[0]
if not os.path.isdir( InDir):
errExit('Input folder does not exist.')
Sequences = cgruSequence( os.listdir( InDir), Options.verbose)
SeqCount = 0
SeqFiles = 0
SeqSize = 0
mkdirs = []
for seq in Sequences:
if not seq['seq']: continue
SeqCount += 1
mkdir = os.path.join( InDir, seq['prefix'].strip( InvalidCharacters + '._ -'))
dir_count = 0
name_with_count = mkdir
while name_with_count in mkdirs:
if not os.path.isfile(afile): continue
files.append(afile)
else:
errorExit('%s not found.' % inarg)
outfolder = Options.output
if outfolder is None:
outfolder = inarg
if arg_is_file:
outfolder = os.path.dirname( outfolder)
else:
outfolder += '%s.%s' % ( ResQual, Options.type )
seqs = cgruSequence(files)
for seq in seqs:
cmd = 'convert'
if Options.afanasy:
cmd += ' -identify -verbose'
elif Options.identify:
cmd += ' -identify'
if seq['seq']:
inseq = '%s%%0%dd%s' % (seq['prefix'],seq['padding'],seq['suffix'])
if Options.afanasy:
cmd += ' "%s[@FIRST@-@LAST@]"' % inseq
else:
cmd += ' "%s[%d-%d]"' % (inseq,seq['first'],seq['last'])
if not os.path.isfile(afile): continue
files.append(afile)
else:
errorExit('%s not found.' % inarg)
outfolder = Options.output
if outfolder is None:
outfolder = inarg
if arg_is_file:
outfolder = os.path.dirname(outfolder)
else:
outfolder += '%s.%s' % (ResQual, Options.type)
seqs = cgruSequence(files)
for seq in seqs:
cmd = 'convert'
if Options.afanasy:
cmd += ' -identify -verbose'
elif Options.identify:
cmd += ' -identify'
if seq['seq']:
inseq = '%s%%0%dd%s' % (seq['prefix'], seq['padding'],
seq['suffix'])
if Options.afanasy:
cmd += ' "%s[@FIRST@-@LAST@]"' % inseq
else:
