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'),
('-f', '--filterid', 'Blast_Filter_Protocol_ID', 'int'),
('-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)
outputs = applyFilterProtocol(options.inputfile,
options.Blast_Filter_Protocol_ID)
protocol = BlastFilterProtocol(options.Blast_Filter_Protocol_ID)
stepsC = len(list(protocol.steps()))
for fn in outputs:
parts = fn.split('.')[-(stepsC+1):][:-1]
rcType = ReadCountType(Name=''.join(parts),
insertIfNeeded=True)
readsC, sequencesC = countFasta(fn)
if readsC == 0 and sequencesC == 0:
raise Exception
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)
