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filter_non_essential_mapqual.py
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filter_non_essential_mapqual.py
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# A script allowing to filter out junctions flagged mapqual when there are
# outside the experimental duplicated parts
##############################IMPORTS##############################
import os
import sys
import getopt
import numpy as np
import pandas as pd
import csv
# Experimentaly, we duplicate part of the genome (chr12 to chr6). This
# lead to trigger the mapqual filter of the translocPipeline for this
# regions. We want to keep these junctions. So we disabled the mapqual
# filter but then we need to remove the "real" mapqual junctions.
def usage():
print('Usage:\n')
print('\tpython ' +
sys.argv[0] + ' -m <metadata file> -g <genome type> -o <output mark> -t <results directory> -n <duplicate file> [-i <input mark>]')
print('\t\t-h or --help : display this help')
print('\t\t-m or --file_metadata : metadata file')
print('\t\t-g or --genome : only filter librairies results with this genome')
print('\t\t-o or --output_mark : mark added to the output file name')
print('\t\t-t or --dir_results : results directory')
print('\t\t-n or --file_duplicate : duplicate positions from the experimental duplicate')
print('\t\t-i or --input_mark : marks from input file')
def main(argv):
file_metadata = ""
genome = ""
output_mark = ""
dir_results = ""
input_mark = ""
file_duplicate = ""
file_input_extension = ""
file_output_extension = ""
try:
opts, args = getopt.getopt(sys.argv[1:], 'm:g:o:t:n:i:', [
'file_metadata=', 'genome=', 'output_mark=', 'dir_results=', 'file_duplicate=', 'input_mark', 'help'])
except getopt.GetoptError:
usage()
sys.exit(2)
##############################OPTIONS##############################
for opt, arg in opts:
if opt in ('-h', '--help'):
usage()
sys.exit(2)
elif opt in ('-m', '--file_metadata'):
file_metadata = arg
elif opt in ('-g', '--genome'):
genome = arg
elif opt in ('-o', '--output_mark'):
output_mark = arg
elif opt in ('-t', '--dir_results'):
dir_results = arg
elif opt in ('-n', '--file_duplicate'):
file_duplicate = arg
elif opt in ('-i', '--input_mark'):
input_mark = arg
else:
print("Error : Bad option -> " + opt)
usage()
sys.exit(2)
##############################CHECK UP/SET UP##############################
# CHECK METADATA FILE
if file_metadata == "" or not os.path.exists(file_metadata):
print("Error : You have to set a metadata file !\n")
usage()
sys.exit(2)
else:
# READ METADATA FILE
metadata = pd.read_table(file_metadata, sep='\t')
# FILTER METADATA FILE IF GENOME INPUT
if genome != "":
metadata = metadata.loc[metadata['Assembly'] == genome]
if metadata.empty:
print("Error : This assembly does not exist in the metadata file !\n")
usage()
sys.exit(2)
else:
print("Error : You have to set a genome name !\n")
usage()
sys.exit(2)
# CHECK RESULTS DIRECTORY
if not os.path.exists(dir_results):
print("Error : You have to set a results directory !\n")
usage()
sys.exit(2)
else:
if dir_results[-1] != "/":
dir_results += "/"
# CHECK INPUT MARKS HISTORY
if input_mark == "":
print("Warning : You will filter the raw file !\n")
# CHECK OUTPUT MARK
if output_mark == "":
print("Error : You have to set an output mark !\n")
usage()
sys.exit(2)
# SELECT INPUT FILES
if input_mark == "":
file_input_extension = ".tlx"
else:
file_input_extension = "_" + "_".join(input_mark.split(",")) + ".tlx"
# TEST IF INPUT EXIST IN AT LEAST ON LIBRARY
check_input_mark = False
for i in metadata['Library'].tolist():
if os.path.exists(dir_results + i + "/" + i + file_input_extension):
check_input_mark = True
if not check_input_mark:
print("Error : Your input marks can not localize a good input file !\n")
usage()
sys.exit(2)
# SELECT OUTPUT FILES
if file_input_extension != "":
file_output_extension = file_input_extension[
:-4] + "_" + output_mark + ".tlx"
else:
file_output_extension = "_" + output_mark + ".tlx"
# CHECK DUPLICATE FILE
if file_duplicate == "" or not os.path.exists(file_duplicate):
print("Error : You have to set a duplicate file !\n")
usage()
sys.exit(2)
else:
# READ DUPLICATE FILE
duplicate_locus = pd.read_table(
file_duplicate, sep='\t', header=None)
for index, row in duplicate_locus.iterrows():
# DONOR CHECK
if row[0][0:3] != 'chr':
print("Error : line." + str(index + 1) +
", col.1 of your duplicate file !\n")
print("Error : Unknown chromosome : " + row[0] + " !\n")
usage()
sys.exit(2)
try:
if int(row[1]) < 1:
print("Error : line." + str(index + 1) +
", col.2 of your duplicate file !\n")
print("Error : Start position has to be positive integer !\n")
usage()
sys.exit(2)
except:
print("Error : line." + str(index + 1) +
", col.2 of your duplicate file !\n")
print("Error : Unknown start position : " +
str(row[1]) + " !\n")
usage()
sys.exit(2)
try:
if int(row[2]) < 1:
print("Error : line." + str(index + 1) +
", col.3 of your duplicate file !\n")
print("Error : End position has to be positive integer !\n")
usage()
sys.exit(2)
except:
print("Error : line." + str(index + 1) +
", col.3 of your duplicate file !\n")
print("Error : Unknown end position : " + str(row[2]) + " !\n")
usage()
sys.exit(2)
if int(row[2]) < int(row[1]):
print("Error : line." + str(index + 1) +
" of your duplicate file !\n")
print("Error : End position is smaller than start position !\n")
usage()
sys.exit(2)
if row[3] != '+' and row[3] != '-':
print("Error : line." + str(index + 1) +
", col.4 of your duplicate file !\n")
print("Error : Unknown strand (+,-) : " + str(row[3]) + " !\n")
usage()
sys.exit(2)
# ACCEPTOR CHECK
if row[4][0:3] != 'chr':
print("Error : line." + str(index + 1) +
", col.5 of your duplicate file !\n")
print("Error : Unknown chromosome : " + row[4] + " !\n")
usage()
sys.exit(2)
try:
if int(row[5]) < 1:
print("Error : line." + str(index + 1) +
", col.6 of your duplicate file !\n")
print("Error : Start position has to be positive integer !\n")
usage()
sys.exit(2)
except:
print("Error : line." + str(index + 1) +
", col.6 of your duplicate file !\n")
print("Error : Unknown start position : " +
str(row[5]) + " !\n")
usage()
sys.exit(2)
try:
if int(row[6]) < 1:
print("Error : line." + str(index + 1) +
", col.7 of your duplicate file !\n")
print("Error : End position has to be positive integer !\n")
usage()
sys.exit(2)
except:
print("Error : line." + str(index + 1) +
", col.7 of your duplicate file !\n")
print("Error : Unknown end position : " + str(row[6]) + " !\n")
usage()
sys.exit(2)
if int(row[6]) < int(row[5]):
print("Error : line." + str(index + 1) +
" of your duplicate file !\n")
print("Error : End position is smaller than start position !\n")
usage()
sys.exit(2)
if row[7] != '+' and row[7] != '-':
print("Error : line." + str(index + 1) +
", col.8 of your duplicate file !\n")
print("Error : Unknown strand (+,-) : " + str(row[7]) + " !\n")
usage()
sys.exit(2)
##############################PRINTS##############################
print('\n-----------------------------------------')
print('Metadata file : ' + file_metadata)
print('Genome : ' + genome)
print('Results directory : ' + dir_results)
print('Duplicate file : ' + file_duplicate)
print('Input file extension: ' + file_input_extension)
print('Output file extension : ' + file_output_extension)
print('-----------------------------------------\n')
##############################PROGRAM##############################
# LOOP OVER EACH LIBRARIES
for library in metadata['Library'].tolist():
print(library)
# CHECK RESULTS DIRECTORY EXISTS
if not os.path.exists(dir_results + library):
print("Warning : " + dir_results +
" does not contains {" + library + "}")
print("Warning : {" + library + "} will not be filtered")
else:
# CHECK INPUT FILE EXISTS
if os.path.exists(dir_results + library + "/" + library + file_input_extension):
file_output = open(dir_results + library + "/" +
library + file_output_extension, 'a')
dataframe_input = pd.read_table(
dir_results + library + "/" + library + file_input_extension, sep='\t')
file_output.write("\t".join(list(dataframe_input)) + "\n")
for index, row in dataframe_input.iterrows():
# IF MAPQUAL
if row.mapqual == 1:
# CHECK IF IN DUPLICATE
if duplicate_locus[(duplicate_locus[0] == row['Rname']) & (duplicate_locus[1] < row['Junction']) & (duplicate_locus[2] > row['Junction'])].empty or duplicate_locus[(duplicate_locus[4] == row['Rname']) & (duplicate_locus[5] < row['Junction']) & (duplicate_locus[6] > row['Junction'])].empty:
pd.DataFrame(row).T.to_csv(
file_output, sep='\t', header=None, index=False)
else:
pd.DataFrame(row).T.to_csv(
file_output, sep='\t', header=None, index=False)
else:
print("Warning : " + dir_results + library + "/" + library +
file_input_extension + " does not exist")
print("Warning : {" + dir_results + library + "/" + library +
file_input_extension + "} will not be filtered")
if __name__ == '__main__':
main(sys.argv[1:])