collateAllStats.py

#!/bin/env python
'''
collateAllStats.py

Copyright (c) 2015, David Edwards, Bernie Pope, Kat Holt
All rights reserved. (see README.txt for more details)

collates the general statistics for set of reads that have gone through
the pipeline during a pangenome run

example:
python collateAllStats.py reference reference_name <example>_rep_cover.txt <outpath> <sequences_string>

Created:	29042013
Modified:	16072014
author: David Edwards
'''
import sys, glob
from pipe_utils import (splitPath)

reference_name = sys.argv[1]
example_rep_cover_File = sys.argv[2]
outpath = sys.argv[3]
sequences_string = sys.argv[4]
sequences = sequences_string.split(',')

example_rep_cover = open(example_rep_cover_File)
replicon_names =[]
for line in example_rep_cover:
    entry = line.split()
    replicon_names.append(entry[0])
example_rep_cover.close()

outfile_allStats_name = outpath + reference_name + '_AllStats.txt'
outfile_allStats_name_user = outpath + reference_name + '_AllStats_user.txt'

output_allStats = ''
header_allStats = 'Isolate\t'
for replicon in replicon_names:
    header_allStats += 'Cover%_' + replicon + '\t'
for replicon in replicon_names:
    header_allStats += 'Depth_' + replicon + '\t'
for replicon in replicon_names:
    header_allStats += 'Mapped%_' + replicon + '\t'
header_allStats += 'Mapped%_Total\tTotal_Reads\tInsert_Mean\tInsert_StDev\tLength_Max\tBase_Qual_Mean\tBase_Qual_StDev\tA_%\tT_%\tG_%\tC_%\tN_%\n'

inFiles = []
for sequence in sequences:
    if sequence != '':
        inFiles.append((outpath+'temp/'+sequence+'/'+sequence+'_AllStats.txt'))

for infile in inFiles:
    allStatsFile = open(infile)
    output_allStats += allStatsFile.read()
    allStatsFile.close()

outfile_allStats = open(outfile_allStats_name,"w")
outfile_allStats.write(header_allStats)
outfile_allStats.writelines(output_allStats)
outfile_allStats.close()

out_lines = []
infile_allStats = open(outfile_allStats_name,"r")
test_line = infile_allStats.readline()
entries = test_line.split()
for i in range(0, len(entries)):
	out_lines.append([entries[i]])
for line in infile_allStats:
	entries = line.split()
	for i in range(0, len(entries)):
		out_lines[i].append(entries[i])
infile_allStats.close()
output = ""
for i in range(0, len(out_lines)):
	for j in range(0, len(out_lines[i])-1):
		output += out_lines[i][j] + "\t"
	output += out_lines[i][-1] + "\n"
outfile_allStats_user = open(outfile_allStats_name_user,"w")
outfile_allStats_user.write(output)
outfile_allStats_user.close()