def count_barcodes(dataset, VERBOSE=0):
'''Count the abundance of each barcode'''
# Get the read filenames
data_filenames = get_raw_read_files(dataset)
datafile = data_filenames['adapter']
# Count the abundance of each barcode
bc_counts = defaultdict(int)
rc = 0
with open(datafile, 'r') as infile:
for read in SeqIO.parse(infile, 'fastq'):
bc_counts[read.seq.tostring()] += 1
rc += 1
if rc == maxreads:
break
print sorted(bc_counts.items(), key=lambda x:x[1], reverse=True)[:20]
# Plot results
plt.figure()
ax=plt.subplot(111)
plt.plot(range(1,len(bc_counts)+1), sorted(bc_counts.values(), reverse=True))
ax.set_yscale('log')
ax.set_xscale('log')
plt.xlabel('barcode rank')
plt.ylabel('abundance')
plt.ion()
plt.show()
if summary:
with open(get_demultiplex_summary_filename(data_folder), 'w') as f:
f.write('Call: python demultiplex.py --run ' + seq_run +
' --verbose ' + str(VERBOSE) + '\n')
adapters_designed = get_adapters_designed(dataset,
VERBOSE=VERBOSE,
summary=summary)
make_output_folders(data_folder,
adapters_designed,
VERBOSE=VERBOSE,
summary=summary)
data_filenames = get_raw_read_files(dataset)
# Is it a dual index library?
if '-' not in adapters_designed[0][0]:
demultiplex_reads_single_index(data_folder,
data_filenames,
adapters_designed,
maxreads=maxreads,
VERBOSE=VERBOSE,
summary=summary)
else:
demultiplex_reads_dual_index(data_folder,
data_filenames,
adapters_designed,
maxreads=maxreads,
VERBOSE=VERBOSE,
# If submit, outsource to the cluster
if submit:
fork_self(seq_run, VERBOSE=VERBOSE, maxreads=maxreads, summary=summary)
sys.exit()
# Specify the dataset
dataset = MiSeq_runs[seq_run]
data_folder = dataset['folder']
if summary:
with open(get_demultiplex_summary_filename(data_folder), 'w') as f:
f.write('Call: python demultiplex.py --run '+seq_run+' --verbose '+str(VERBOSE)+'\n')
adapters_designed = get_adapters_designed(dataset, VERBOSE=VERBOSE, summary=summary)
make_output_folders(data_folder, adapters_designed, VERBOSE=VERBOSE,
summary=summary)
data_filenames = get_raw_read_files(dataset)
# Is it a dual index library?
if '-' not in adapters_designed[0][0]:
demultiplex_reads_single_index(data_folder, data_filenames, adapters_designed,
maxreads=maxreads, VERBOSE=VERBOSE,
summary=summary)
else:
demultiplex_reads_dual_index(data_folder, data_filenames, adapters_designed,
maxreads=maxreads, VERBOSE=VERBOSE,
summary=summary)