hashobject = Fastq_Reader(inputdir, outputdir)
Read_Partitions = glob.glob(os.path.join(hashobject.input_path, '*.fastq'))
Read_Partitions = [
fp for fp in Read_Partitions
if ('.pairs.' not in fp) and ('.singleton.' not in fp)
]
Read_Partitions = list(
set([
fp[fp.rfind('/') + 1:fp.index('.cluster') + 8]
for fp in Read_Partitions
]))
Processed_Partitions = glob.glob(
os.path.join(hashobject.output_path, '*.cluster_velvet/contigs.fa'))
Processed_Partitions = [
fp[len(hashobject.output_path):fp.index('.cluster') + 8]
for fp in Processed_Partitions
]
rp = Read_Partitions[fr]
if rp not in Processed_Partitions:
f = open(libdir + 'samples_grouped_by_lib.csv')
reader = csv.reader(f)
hashobject.sample_library = {}
i = 0
for row in reader:
for sample in row:
hashobject.sample_library[sample] = i
i += 1
f.close()
hashobject.num_libs = i
hashobject.process_cluster(rp)
inputdir = arg
if inputdir[-1] != '/':
inputdir += '/'
elif opt in ('-o','--outputdir'):
outputdir = arg
if outputdir[-1] != '/':
outputdir += '/'
elif opt in ('-l','--libdir'):
libdir = arg
if libdir[-1] != '/':
libdir += '/'
hashobject = Fastq_Reader(inputdir,outputdir)
Read_Partitions = glob.glob(os.path.join(hashobject.input_path,'*.fastq'))
Read_Partitions = [fp for fp in Read_Partitions if ('.pairs.' not in fp) and ('.singleton.' not in fp)]
Read_Partitions = list(set([fp[fp.rfind('/')+1:fp.index('.cluster')+8] for fp in Read_Partitions]))
Processed_Partitions = glob.glob(os.path.join(hashobject.output_path,'*.cluster_velvet/contigs.fa'))
Processed_Partitions = [fp[len(hashobject.output_path):fp.index('.cluster')+8] for fp in Processed_Partitions]
rp = Read_Partitions[fr]
if rp not in Processed_Partitions:
f = open(libdir+'samples_grouped_by_lib.csv')
reader = csv.reader(f)
hashobject.sample_library = {}
i = 0
for row in reader:
for sample in row:
hashobject.sample_library[sample] = i
i += 1
f.close()
hashobject.num_libs = i
hashobject.process_cluster(rp)
