https://github.com/fjruizruano/ngs-protocols
Tip revision: 39a091d1fa569a7fc717ac73c4b3de07f0a1204d authored by fjruizruano on 03 August 2023, 11:48:27 UTC
adding gfa2fas.py and extract_gfa.py
adding gfa2fas.py and extract_gfa.py
Tip revision: 39a091d
extract_reads_rm.py
#!/usr/bin/python
import sys
try:
data = sys.argv[1]
names = sys.argv[2]
except:
data = raw_input("RepeatMasker's *.out file: ")
names = raw_input("List with names: ")
d = open(data).readlines()
n = open(names).readlines()
li = []
for i in range(0,len(n)):
n[i] = n[1][:-1]
for line in d[3:]:
line = line.split()
if line[10] in n:
li.append(line[4][:-1])
li = set(li)
w = open(names+".lst","w")
for l in li:
w.write("%s\n%s\n" % (l+"1",l+"2"))
w.close()