#!/usr/bin/env python

__author__ = 'Francesco Asnicar (f.asnicar@unitn.it)'

__version__ = '0.4'

__date__ = '24 March 2019'

import sys

import os

import glob

import argparse

import shutil

if sys.version_info[0] < 3:

raise Exception("Not running Python3")

def info(s, init_new_line=False, exit=False, exit_value=0):

if init_new_line:

sys.stdout.write('\n')

sys.stdout.write('{}'.format(s))

sys.stdout.flush()

if exit:

sys.exit(exit_value)

def error(s, init_new_line=False, exit=False, exit_value=1):

if init_new_line:

sys.stderr.write('\n')

sys.stderr.write('[e] {}\n'.format(s))

sys.stderr.flush()

if exit:

sys.exit(exit_value)

def read_params():

p = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)

p.add_argument('-i', '--input_folder', required=True, type=str,

help="Input folder containing the samples' folders to rename")

p.add_argument('-o', '--output_folder', required=True, type=str,

help="Output folder where move the renamed folders/files")

p.add_argument('-m', '--mapping_file', required=True, type=str,

help='The mapping file containing the sample name and the forward and '

'reverse indexes associated')

p.add_argument('-s', '--separator', default='\t', type=str,

help='The column separator in the mapping file')

p.add_argument('-1', '--index_primer_1', default=2, type=int,

help='The column of the Index primer 1')

p.add_argument('-2', '--index_primer_2', default=1, type=int,

help='The column of the Index primer 2')

p.add_argument('-n', '--sample_name', default=0, type=int,

help='The column of the Sample IDs')

return p.parse_args()

def check_params(args):

if not os.path.isdir(args.input_folder):

error('', exit=True)

if not os.path.isfile(args.mapping_file):

error('', exit=True)

if len(args.separator) > 1:

error('', exit=True)

def read_mapping_file(map_file, sep, sn, i1, i2):

mapp = {}

sample_names = []

with open(map_file) as f:

for row in f:

if row.startswith('#'):

continue

row_clean = row.strip().split(sep)

if (row_clean[i1], row_clean[i2]) not in mapp:

mapp[(row_clean[i1], row_clean[i2])] = row_clean[sn].replace(' ', '_')

sample_names.append(row_clean[sn].replace(' ', '_'))

else:

error('indexes "({},{})" already present, duplicated?'

.format(row_clean[i1], row_clean[i2]), exit=True)

if len(sample_names) != len(set(sample_names)):

error('there are duplicated sample names, check your mapping file', exit=True)

return mapp

def demultiplex(input_folder, output_folder, mapping):

for fld in glob.iglob(os.path.join(input_folder, '*')):

if not os.path.isdir(fld):

continue

fld_name = os.path.basename(fld)

new_name = None

for (i1, i2), v in mapping.items():

if (i1 in fld_name) and (i2 in fld_name):

new_name = v

break

if not new_name:

# error('skipping "{}", no indexes found in mapping'.format(fld))

continue

output = os.path.join(output_folder, new_name)

if os.path.isdir(output):

error('skipping "{}", folder already exists'.format(output))

continue

else:

info('Creating folder "{}"\n'.format(output))

os.mkdir(output, mode=0o775)

for src in (glob.glob(os.path.join(fld, '*_R1.fastq.bz2')) +

glob.glob(os.path.join(fld, '*_R2.fastq.bz2')) +

glob.glob(os.path.join(fld, '*_UN.fastq.bz2')) +

glob.glob(os.path.join(fld, '*_summary.stats'))):

suffix = src.split('_')[-1]

dest = os.path.join(output, new_name + '_' + suffix)

info('Copying "{}" into "{}"\n'.format(src, dest))

shutil.copy2(src, dest)

if __name__ == "__main__":

args = read_params()

check_params(args)

mapp = read_mapping_file(args.mapping_file, args.separator, args.sample_name,

args.index_primer_1, args.index_primer_2)

demultiplex(args.input_folder, args.output_folder, mapp)

sys.exit(0)