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interesect_bed_compare.py
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interesect_bed_compare.py
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#!/usr/bin/env python
# Upendra Kumar Devisetty
# 12/15/15
# Script to parse Bedtools closest ouput
import sys
file = open(sys.argv[1]) #intersect file
file_2 = open(sys.argv[2]) #lincRNA_final_transcripts.fa
file_3 = open(sys.argv[3], "w") #lincRNA_overlapping_known_final_transcripts.fa
result = []
dic = {}
for line in file:
line = line.strip().split("\t")
test = line[9]
new = str.split(test, " ")
final = new[3]
final2 = final[:-2]
final3 = final2[1:]
result.append(final3)
for line in file_2:
line = line.strip()
if line.startswith(">"):
line = line[1:]
id = line
dic[id] = " "
else:
dic[id] += line
for ele in set(result):
for kee, val in dic.items():
new = "_overlapping_known_lncRNA"
if ele in kee:
kee2 = kee+new
dic[kee2] = dic[kee]
del dic[kee]
for kee2, val2 in dic.items():
kee2 = ">"+kee2
val2 = val2.lstrip()
file_3.write(kee2)
file_3.write("\n")
file_3.write(val2)
file_3.write("\n")