Question

我在文本文件中有序列如下

＆GT; P1

MPPRRSIVEVKVLDVQKRRVPNKHYVYIIRVTWSSGATEAIYRRYSKFFDLQMQMLDKFP MEGGQKDPKQRIIPFLPGKILFRRSHIRDVAVKRLIPIDEYCKALIQLPPYISQCDEVLQ FFETRPEDLNPPKEEHIGKKKSGNDPTSVDPMVLEQYVVVADYQKQESSEISLSVGQVVD IIEKNESGWWFVSTAEEQGWVPATCLEGQDGVQDEFSLQPEEEEKYTVIYPYTARDQDEM NLERGAVVEVVQKNLEGWWKIRYQGKEGWAPASYLKKNSGEPLPPKLGPSSPAHSGALDL DGVSRHQNAMGREKELLNNQRDGRFEGRLVPDGDVKQRSPKMRQRPPPRRDMTIPRGLNL

＆GT; P2

MAEVRKFTKRLSKPGTAAELRQSVSEAVRGSVVLEKAKLVEPLDYENVITQRKTQIYSDP LRDLLMFPMEDISISVIGRQRRTVQSTVPEDAEKRAQSLFVKECIKTYSTDWHVVNYKYE DFSGDFRMLPCKSLRPEKIPNHVFEIDEDCEKDEDSSSLCSQKGGVIKQGWLHKANVNST ITVTMKVFKRRYFYLTQLPDGSYILNSYKDEKNSKESKGCIYLDACIDVVQCPKMRRHAF ELKMLDKYSHYLAAETEQEMEEWLIMLKKIIQINTDSLVQEKKDTVEAIQEEETSSQGKA ENIMASLERSMHPELMKYGRETEQLNKLSRGDGRQNLFSFDSEVQRLDFSGIEPDVKPFE EKCNKRFMVNCHDLTFNILGHIGDNAKGPPTNVEPFFINLALFDVKNNCKISADFHVDLN PPSVREMLWGTSTQLSNDGNAKGFSPESLIHGIAESQLCYIKQGIFSVTNPHPEIFLVVR

＆GT; P3

GDDSEWLKLPVDQKCEHKLWKARLSGYEEALKIFQKIKDEKSPEWSKYLGLIKKFVTDS NAVVQLKGLEAALVYVENAHVAGKTTGEVVSGVVSKVFNQPKAKAKELGIEICLMYVEIE KGESVQEELLKGLDNKNPKIIVACIETLRKALSEFGSKIISLKPIIKVLPKLFESRDKAV RDEAKLFAIEIYRWNRDAVKHTLQNINSVQLKELEEEWVKLPTGAPKPSRFLRSQQELEA KLEQQQSAGGDAEGGGDDGDEVPQVDAYELLDAVEILSKLPKDFYDKIEAKKWQERKEAL EAVEVLVKNPKLEAGDYADLVKALKKVVGKDTNVMLVALAAKCLTGLAVGLRKKFGQYAG HVVPTILEKFKEKKPQVVQALQEAIDAIFLTTTLQNISEDVLAVMDNKNPTIKQQTSLFI ARSFRHCTSSTLPKSLLKPFCAALLKHINDSAPEVRDAAFEALGTALKVVGEKSVNPFLA

。。。。。

总共100个序列在这些序列中，我使用python脚本搜索了一个感兴趣的模式，如下所示

import re

infile=open("seq.fasta",'r')

out=open("results.csv",'w')
pattern=re.compile(r"(P[A-Z]{2}P)")
for line in infile:
    line = line.strip("\n")
    if line.startswith('>'):
        name=line
    else:
        s = re.findall(pattern,line)
    print '%s:%s' %(name,s)
    out.write('%s:\t%s\n' %(name,s))

这个脚本完美的工作它给了我想要的模式我希望...现在我想计算每个序列中感兴趣的模式目前的脚本输出如下

＆GT;

p1：PGCP

＆GT;

p1：PHCP，PKCP。。。等等

但我想按照以下说明＆gt;

p1：1

＆GT;

p1：2。。。

有人可以告诉我如何使用python

来做到这一点

Answer 1

findall方法返回匹配字符串列表。因此，您只需在代码中使用len(s)而不是s。

out.write('%s:\t%s\n' %(name,len(s)))

计算序列中的模式

1 个答案: