小编Ire*_*rek的帖子

我挖掘了许多线索,但他们都没有解决这个问题.

我感兴趣的是addind string chr到每一行的列的开头.文件是制表符分隔的,看起来像:

re1 1   AGT
re2 1   AGT
re3 2   ACGTCA
re12    3   ACGTACT

我需要的是:

re1 chr1    AGT
re2 chr1    AGT
re3 chr2    ACGTCA
re12    chr3    ACGTACT

可以在bash oneliner上

非常感谢任何帮助,欢呼,Irek

我有一个代码如下:

import HTSeq
reference = open('genome.fa','r')
sequences = dict( (s.name, s) for s in HTSeq.FastaReader(reference))
out = open('homopolymers_in_ref','w')

def find_all(a_str,sub):
    start = 0
    while True:
        start = a_str.find(sub, start)
        if start == -1: return
        yield start
        start += len(sub)
homa = 'AAAAAAAAAA'
homc = 'CCCCCCCCCC'
homg = 'GGGGGGGGGG'
homt = 'TTTTTTTTTT'
for key,line in sequences.items():
    seq = str(line)
    a= list(find_all(seq,homa))
    c = list(find_all(seq,homc))
    g = list(find_all(seq,homg))
    t = list(find_all(seq,homt))
    for i in a:
##        print i,key,'A'
        out.write(str(i)+'\t'+str(key)+'\t'+'A'+'\n')
    for i in …