#!/usr/bin/env python

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

'Paolo Manghi (paolo.manghi@unitn.it)')

__version__ = '0.3'

__date__ = '2 May 2018'

import sys

import os

import glob

import argparse

import numpy as np

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_dir', required=True, default=None, type=str,

help='Input folder containing the files to cat')

p.add_argument('-e', '--extension', required=False, default=".stats", type=str,

help='The extension of the files to cat')

p.add_argument('-o', '--output_file', required=True, default=None, type=str,

help='The output file to write')

p.add_argument('--inp_sep', required=False, default="\t", type=str,

help='Define the field-separator character for the input files')

p.add_argument('--out_sep', required=False, default="\t", type=str,

help='Define the field-separator character for the output file')

return p.parse_args()

def check_params(args):

if not args.input_dir.endswith('/'):

args.input_dir += '/'

if not args.extension.startswith('.'):

args.extension = '.' + args.extension

if len(args.inp_sep) > 1:

error('input field-separator is more than one characther, "{}"'.format(args.inp_sep), exit=True)

if len(args.out_sep) > 1:

error('output field-separator is more than one characther, "{}"'.format(args.out_sep), exit=True)

def cat(input_dir, ext, inp_sep, output_file):

header = None

data = []

for stat_file in sorted(glob.glob(input_dir + '*' + ext)):

if os.path.basename(stat_file) == os.path.basename(output_file): # should check not to include the output file

continue

with open(stat_file) as f:

for row in f:

if not header and row.startswith('#'):

header = row.strip().split(inp_sep)

if not row.startswith('#'):

data.append(row.strip().split(inp_sep))

if header:

data = [header] + data

return data

def line_of_interest(sample_id):

return (sample_id.endswith('_R1.fastq') or sample_id.endswith('_R2.fastq') or

sample_id.endswith('_UN.fastq') or sample_id.endswith('_UP.fastq'))

def line_to_str_or_float(line):

return [float(f) if str(f)[-1].isdigit() else str(f) for f in line]

def summarize(data):

funcs = {'n_of_bases': sum,

'n_of_reads': sum,

'min_read_len': min,

'median_read_len': np.median,

'mean_read_len': np.mean,

'max_read_len': max}

convs = {'n_of_bases': int,

'n_of_reads': int,

'min_read_len': int,

'median_read_len': float,

'mean_read_len': float,

'max_read_len': int}

interesting_lines = [line_to_str_or_float(line) for line in data if line_of_interest(line[0])]

for pos, fld in enumerate(data[0]):

if pos == 0:

summary = ['_'.join(interesting_lines[0][0].split('_')[:-1])]

else:

summary += [convs[fld](funcs[fld]([field[pos] for field in interesting_lines]))]

return data + [summary]

def write_output_file(output_file, out_sep, data):

if os.path.isfile(output_file):

error('output file "{}" already exists'.format(output_file), exit=True)

with open(output_file, 'w') as f:

f.write('\n'.join([out_sep.join(map(str, a)) for a in data]) + '\n')

if __name__ == "__main__":

args = read_params()

check_params(args)

data = summarize(cat(args.input_dir, args.extension, args.inp_sep, args.output_file))

write_output_file(args.output_file, args.out_sep, data)

sys.exit(0)