elif opt in ('-o','--outputdir'):
outputdir = arg
if outputdir[-1] != '/':
outputdir += '/'
elif opt in ('-z','--reversecomp'):
do_reverse_compliment = False
FP = glob.glob(os.path.join(inputdir,'*.fastq.*'))
if len(FP) == 0:
# single file per-sample
FP = glob.glob(os.path.join(inputdir,'*.fastq'))
file_prefix = FP[fr]
file_split = file_prefix[file_prefix.index('.fastq')+6:]
file_prefix = file_prefix[file_prefix.rfind('/')+1:file_prefix.index('.fastq')]
hashobject = Fastq_Reader(inputdir,outputdir)
f = open(hashobject.input_path+file_prefix+'.fastq'+file_split,'r')
read_type = hashobject.id_type(f)
g = gzip.open(hashobject.output_path+file_prefix+'.hashq'+file_split+'.gz','wb')
hashobject.hpfx = hashobject.hpfx + str(hashobject.kmer_size)+','
A = []
reads_hashed = 0
while A != None:
try:
A,B = hashobject.generator_to_bins(hashobject.read_generator(f,max_reads=25000,verbose_ids=True),rc=do_reverse_compliment)
for b in range(len(B)):
reads_hashed += kmer_bins(B[b],A,hashobject.hpfx,g,read_type)
except Exception,err:
pass
#print str(err)
f.close()
g.close()
print 'total reads hashed:',reads_hashed
do_reverse_compliment = False
FP = glob.glob(os.path.join(inputdir, '*.fastq.*'))
if len(FP) == 0:
# single file per-sample
FP = glob.glob(os.path.join(inputdir, '*.fastq'))
file_prefix = FP[fr]
file_split = file_prefix[file_prefix.index('.fastq') + 6:]
file_prefix = file_prefix[file_prefix.rfind('/') +
1:file_prefix.index('.fastq')]
hashobject = Fastq_Reader(inputdir, outputdir)
f = open(hashobject.input_path + file_prefix + '.fastq' + file_split, 'r')
read_type = hashobject.id_type(f)
g = gzip.open(
hashobject.output_path + file_prefix + '.hashq' + file_split + '.gz',
'wb')
hashobject.hpfx = hashobject.hpfx + str(hashobject.kmer_size) + ','
A = []
reads_hashed = 0
while A != None:
try:
A, B = hashobject.generator_to_bins(hashobject.read_generator(
f, max_reads=25000, verbose_ids=True),
rc=do_reverse_compliment)
for b in range(len(B)):
reads_hashed += kmer_bins(B[b], A, hashobject.hpfx, g,
read_type)
except Exception, err:
pass
#print str(err)
f.close()
g.close()
