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Copy pathappend_bed_name.py
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append_bed_name.py
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#!/usr/bin/python
import regex
import csv
import sys
import getopt
def main(argv):
inputfile=[]
bedfile=[]
outputfile=[]
try:
opts, args = getopt.getopt(argv,"hi:o:b:",["ifile=","ofile=","bfile="])
except getopt.GetoptError:
print 'append_bed_name.py -i <input_gatk_depthOfCoverage_file> -o <appended_file> -b <bed_file_with_name_in_column_4>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'append_bed_name.py -i <input_gatk_depthOfCoverage_file> -o <appended_file> -b <bed_file_with_name_in_column_4>'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
print outputfile
elif opt in ("-b", "--bfile"):
bedfile = arg
print str(outputfile)
print str(inputfile)
f = open(outputfile,'wt')
f2 = open(bedfile,'rb')
bed_reader=csv.reader(f2,delimiter="\t")
#with open(inputfile,'rb') as tsvfile:
# reader=csv.DictReader(tsvfile,delimiter="\t")
#fieldnames=['Name','Target','total_coverage','average_coverage','libA_total_cvg','libB_total_cvg',
# 'libA_mean_cvg','libB_mean_cvg','libA_%_above_250','libB_%_above_250'
# ,'libA_%_above_500','libB_%_above_500'
# ,'libA_%_above_1000','libB_%_above_1000']
#writer= csv.DictWriter(f,delimiter="\t",fieldnames=fieldnames)
#writer.writeheader()
#iteration=0
#for row in reader:
#print((row['Otherinfo']))
#if iteration!=0:
# bed_row=bed_reader.next()
# bed_row=bed_reader.next()
# row['Name']=bed_row[3]
# writer.writerow({'Name': bed_row[3], 'Target': row['Target'], 'total_coverage': row['total_coverage'],'average_coverage': row['average_coverage'],
# 'libA_total_cvg':row['libA_total_cvg'],'libB_total_cvg':row['libB_total_cvg'],
# 'libA_mean_cvg': row['libA_mean_cvg'],'libB_mean_cvg':row['libB_mean_cvg']
# ,'libA_%_above_250':row['libA_%_above_250'],'libB_%_above_250':row['libB_%_above_250']
# ,'libA_%_above_500': row['libA_%_above_500'],'libB_%_above_500':row['libB_%_above_500']
# ,'libA_%_above_1000': row['libA_%_above_1000'],'libB_%_above_1000':row['libB_%_above_1000']})
#f.close()
#f2.close()
with open(inputfile,'rb') as tsvfile:
reader=csv.DictReader(tsvfile,delimiter="\t")
fieldnames=['Name','Target','total_coverage','average_coverage'
,'total_%_above_500','total_%_above_1000']
writer= csv.DictWriter(f,delimiter="\t",fieldnames=fieldnames)
writer.writeheader()
iteration=0
for row in reader:
#print((row['Otherinfo']))
#if iteration==1:
bed_row=bed_reader.next()
#else:
# iteration=1
# continue
writer.writerow({'Name': bed_row[3], 'Target': row['Target'], 'total_coverage': row['total_coverage'],'average_coverage': row['average_coverage']
,'total_%_above_500': row['total_%_above_500'],'total_%_above_1000':row['total_%_above_1000']})
f.close()
f2.close()
#with open(inputfile,'rb') as tsvfile:
# reader=csv.reader(tsvfile,delimiter="\t")
# writer= csv.writer(f,delimiter="\t")
# iteration=0
# for row in reader:
#print((row['Otherinfo']))
# newrow=row[::-1]
# if iteration!=0:
# bed_row=bed_reader.next()
# newrow.append(bed_row[3])
# else:
# newrow.append('Name')
# iteration=1
# newrow=newrow[::-1]
# writer.writerow(newrow)
#f.close()
#f2.close()
if __name__ == "__main__":
main(sys.argv[1:])