https://github.com/fjruizruano/ngs-protocols
Revision 6c3c041f237f2a54076663591a1779db18409d37 authored by fjruizruano on 04 May 2018, 22:30:12 UTC, committed by fjruizruano on 04 May 2018, 22:30:12 UTC
1 parent 14d1b7e
Tip revision: 6c3c041f237f2a54076663591a1779db18409d37 authored by fjruizruano on 04 May 2018, 22:30:12 UTC
adding annot_to_rexp.py
adding annot_to_rexp.py
Tip revision: 6c3c041
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()
Computing file changes ...
