def main(args):
parser = OptionParser('usage: %prog [options]')
optionsAvailable = (
('-i', '--input', 'inputfile', 'string'),
('-o', '--output', 'outputfile', 'string'),
('-a', '--alignment', 'Alignment_Protocol_ID', 'int'),
)
for oa in optionsAvailable:
parser.add_option(oa[0], oa[1], dest=oa[2], type=oa[3])
(options, args) = parser.parse_args(args)
ap = AlignmentProtocol(options.Alignment_Protocol_ID)
cArgs = ap.Arguments % {'database': ap.Database_Path}
cArgs = cArgs.split(' -')
cArgs = [cArgs[0],] + map(lambda x: '-' + x, cArgs[1:])
cArgs.extend(('-i%s' % options.inputfile,
'-o%s' % options.outputfile))
rc = runCommand((ap.Program, ) + tuple(cArgs), True)[1]
if rc != 0:
raise Exception
failed = True
if os.path.exists(options.outputfile):
content = open(options.inputfile).read()
nEntries = len(re.findall(r'^>', content, re.M))
lastLine = runCommand(('tail', '-n1', options.outputfile))
match = re.match(r'^#(?:.*)finished(?:.*) (\d+) (?:.*)',
lastLine)
failed = match is None or int(match.group(1)) != nEntries
if failed:
return 1
return 0
def main(args):
parser = OptionParser('usage: %prog [options]')
optionsAvailable = (
('-i', '--input', 'inputfile', 'string'),
('-o', '--output', 'outputfile', 'string'),
('-s', '--sequencefileid', 'Sequence_File_ID', 'int'),
)
for oa in optionsAvailable:
parser.add_option(oa[0], oa[1], dest=oa[2], type=oa[3])
(options, args) = parser.parse_args(args)
outfn = options.outputfile.replace('.fasta','')
out, rc = runCommand((FASTA_FILTER_PATH, '-r0.4', '-H18', '-a:4',
'-A0', '--output=%s' % outfn,
options.inputfile), True)
if rc != 0:
raise Exception
readsC, sequencesC = countFasta(options.outputfile)
if int(readsC) == 0 and int(sequencesC) == 0:
print readsC, sequencesC
raise Exception
rcType = ReadCountType(Name='qualityFiltered',
insertIfNeeded=True)
ReadCount(Sequence_File_ID=options.Sequence_File_ID,
Reads=readsC, Sequences=sequencesC,
Read_Count_Type_ID=rcType, insertIfNeeded=True)
def main(args):
parser = OptionParser('usage: %prog [options]')
optionsAvailable = (
('-i', '--input', 'inputfile', 'string'),
('-o', '--output', 'outputfile', 'string'),
('-s', '--sequencefileid', 'Sequence_File_ID', 'int'),
)
for oa in optionsAvailable:
parser.add_option(oa[0], oa[1], dest=oa[2], type=oa[3])
(options, args) = parser.parse_args(args)
runCommand((FASTA_FILTER_PATH, '-Q', '-d', options.inputfile))
output = '.'.join((os.path.splitext(options.inputfile)[0],
'noDups', 'fastq'))
readsC, sequencesC = countFasta(options.outputfile)
if readsC == 0 and sequencesC == 0:
raise Exception
rcType = ReadCountType(Name='noDups', insertIfNeeded=True)
ReadCount(Sequence_File_ID=options.Sequence_File_ID,
Reads=readsC, Sequences=sequencesC,
Read_Count_Type_ID=rcType, insertIfNeeded=True)
