解析 txt 文件并根据列表提取特定部分

Question

我需要帮助才能提取 txt.file 的一部分，例如

#some comments
#some comments
#some comments
# Predicted genes for sequence number 1 on both strands
# start gene g1
scaffold_0  AUGUSTUS    gene    1268    6647    0.19    -   .   g1
scaffold_0  AUGUSTUS    transcript  1268    6647    0.19    -   .   g1.t1
scaffold_0  AUGUSTUS    stop_codon  1268    1270    .   -   0   transcript_id "g1.t1"; gene_id "g1";
scaffold_0  AUGUSTUS    intron  1457    6004    0.62    -   .   transcript_id "g1.t1"; gene_id "g1";
scaffold_0  AUGUSTUS    intron  6194    6509    0.42    -   .   transcript_id "g1.t1"; gene_id "g1";
scaffold_0  AUGUSTUS    CDS 1268    1456    0.62    -   0   transcript_id "g1.t1"; gene_id "g1";
scaffold_0  AUGUSTUS    CDS 6005    6193    0.52    -   0   transcript_id "g1.t1"; gene_id "g1";
scaffold_0  AUGUSTUS    CDS 6510    6647    0.3 -   0   transcript_id "g1.t1"; gene_id "g1";
scaffold_0  AUGUSTUS    start_codon 6645    6647    .   -   0   transcript_id "g1.t1"; gene_id "g1";
# protein sequence = [MDASLTLHRFRKRGAKRCGISDLKDIRNALRVGEIGPELLQSLATRGLLKKVDCNLVRIWSHMTRQKKKFFEIRVSYH
# HVRTTSKSKLLLVPDTNPDAALQKKMSTRLCTRYGYAITGQRGEIRKIRREMDGQSERQIDGRTHSRAGHLPTDKPSKGAKRCNFSISTFKTV]
# end gene g1
###
# start gene g2
scaffold_0  AUGUSTUS    gene    10257   16732   0.03    -   .   g2
scaffold_0  AUGUSTUS    transcript  10257   16732   0.03    -   .   g2.t1
scaffold_0  AUGUSTUS    stop_codon  10257   10259   .   -   0   transcript_id "g2.t1"; gene_id "g2";
scaffold_0  AUGUSTUS    intron  10476   12506   0.18    -   .   transcript_id "g2.t1"; gene_id "g2";
scaffold_0  AUGUSTUS    intron  12667   15174   0.18    -   .   transcript_id "g2.t1"; gene_id "g2";
scaffold_0  AUGUSTUS    intron  15183   16579   0.2 -   .   transcript_id "g2.t1"; gene_id "g2";
scaffold_0  AUGUSTUS    CDS 10257   10475   0.59    -   0   transcript_id "g2.t1"; gene_id "g2";
scaffold_0  AUGUSTUS    CDS 12507   12666   0.48    -   1   transcript_id "g2.t1"; gene_id "g2";
scaffold_0  AUGUSTUS    CDS 15175   15182   0.21    -   0   transcript_id "g2.t1"; gene_id "g2";
scaffold_0  AUGUSTUS    CDS 16580   16732   0.34    -   0   transcript_id "g2.t1"; gene_id "g2";
scaffold_0  AUGUSTUS    start_codon 16730   16732   .   -   0   transcript_id "g2.t1"; gene_id "g2";
# protein sequence = [MLAASRYSRRSRKISRVQHWDVNDSRDISACNSLSSEKAPSVTRREWHEMRLLSRSRDRFADCLRTVAARVRGPIKPS
# PCSGRQCETVRWRIENGPLLTDQLAVFAQVRLALASTTSGQHPSGDNVGNDRYATRLYLLTSRGTSLVHRGNELKFDRRRWTNLSTILVYANEILRCE
# EGW]
# end gene g2
###
# start gene g3
scaffold_0  AUGUSTUS    gene    21625   24883   0.55    -   .   g3
scaffold_0  AUGUSTUS    transcript  21625   24883   0.55    -   .   g3.t1
scaffold_0  AUGUSTUS    stop_codon  21625   21627   .   -   0   transcript_id "g3.t1"; gene_id "g3";
scaffold_0  AUGUSTUS    intron  21830   22738   0.68    -   .   transcript_id "g3.t1"; gene_id "g3";
scaffold_0  AUGUSTUS    intron  22760   22851   0.61    -   .   transcript_id "g3.t1"; gene_id "g3";
scaffold_0  AUGUSTUS    intron  22954   24665   0.89    -   .   transcript_id "g3.t1"; gene_id "g3";
scaffold_0  AUGUSTUS    CDS 21625   21829   0.91    -   1   transcript_id "g3.t1"; gene_id "g3";
scaffold_0  AUGUSTUS    CDS 22739   22759   0.68    -   1   transcript_id "g3.t1"; gene_id "g3";
scaffold_0  AUGUSTUS    CDS 22852   22953   0.84    -   1   transcript_id "g3.t1"; gene_id "g3";
scaffold_0  AUGUSTUS    CDS 24666   24883   0.84    -   0   transcript_id "g3.t1"; gene_id "g3";
scaffold_0  AUGUSTUS    start_codon 24881   24883   .   -   0   transcript_id "g3.t1"; gene_id "g3";
# protein sequence = [MEYSQIFSPKLQVLSTKERLLTGNRTNISLENTRLGASIELGNPIHKWKPVAEQGSLGIEPSDGSSSLHDLPLYFRTR
# CETSNASTSDRIRKLTIREGKGFDDSQMTCMLIVDKPPKKTLTTLDKEWKEISIRMTTKVISRCDMAANEEDEDSSESIYHAPFEDAPCTVRTSLNFD
# TSALE]
# end gene g3
###

所以首先我有一个列表，例如list_gene_names=['g1','g3']

我想遍历该列表并提取蛋白质序列（在括号之间）并将它们放入一个名为的文件中： sequence_file.fa

到目前为止，我尝试过：

file_to_parse=open('file_to_parse.txt','w')

with open("sequence_file.fa",'a') as sequence_file_output:
  for names in list_gene_names:
    (then we should locate the part between '''# start gene names''' and '''# end gene names''')
    and get the part '''# protein sequence =''' between brackets"
    print('>',names,file=sequence_file_output,sep='')
    print(part_between_brackets,file=sequence_file_output)

最后，文件sequence_file.fa应如下所示：

>g1
MDASLTLHRFRKRGAKRCGISDLKDIRNALRVGEIGPELLQSLATRGLLKKVDCNLVRIWSHMTRQKKKFFEIRVSYHHVRTTSKSKLLLVPDTNPDAALQKKMSTRLCTRYGYAITGQRGEIRKIRREMDGQSERQIDGRTHSRAGHLPTDKPSKGAKRCNFSISTFKTV
>g2
MEYSQIFSPKLQVLSTKERLLTGNRTNISLENTRLGASIELGNPIHKWKPVAEQGSLGIEPSDGSSSLHDLPLYFRTRCETSNASTSDRIRKLTIREGKGFDDSQMTCMLIVDKPPKKTLTTLDKEWKEISIRMTTKVISRCDMAANEEDEDSSESIYHAPFEDAPCTVRTSLNFDTSALE
  

感谢您的帮助和时间

Answer 1

正则表达式将是一种方式：

import re

regex = r"# start gene(.+?)$[^[]*\[([^\]]*)\]"

with open("sequence_file.fa",'a') as sequence_file_output:
    test_str = sequence_file_output.read()

matches = re.finditer(regex, test_str, re.MULTILINE | re.DOTALL)
with open("result.txt","w") as f:
  for matchNum, match in enumerate(matches, start=1):
      # restrict to g1,g2:
      if match.group(1).strip() in "g1,g2":  
          for groupNum in range(1, len(match.groups())+1):
              f.write(match.group(groupNum).replace("#",
                  "").replace(" ","").replace("\n",""))
              f.write("\n")

with open("result.txt") as f:
  print(f.read())

Output：

g1
MDASLTLHRFRKRGAKRCGISDLKDIRNALRVGEIGPELLQSLATRGLLKKVDCNLVRIWSHMTRQKKKFFEIRVSYHHVRTTSKSKLLLVPDTNPDAALQKKMSTRLCTRYGYAITGQRGEIRKIRREMDGQSERQIDGRTHSRAGHLPTDKPSKGAKRCNFSISTFKTV
g2
MLAASRYSRRSRKISRVQHWDVNDSRDISACNSLSSEKAPSVTRREWHEMRLLSRSRDRFADCLRTVAARVRGPIKPSPCSGRQCETVRWRIENGPLLTDQLAVFAQVRLALASTTSGQHPSGDNVGNDRYATRLYLLTSRGTSLVHRGNELKFDRRRWTNLSTILVYANEILRCEEGW
g3
MEYSQIFSPKLQVLSTKERLLTGNRTNISLENTRLGASIELGNPIHKWKPVAEQGSLGIEPSDGSSSLHDLPLYFRTRCETSNASTSDRIRKLTIREGKGFDDSQMTCMLIVDKPPKKTLTTLDKEWKEISIRMTTKVISRCDMAANEEDEDSSESIYHAPFEDAPCTVRTSLNFDTSALE

正则表达式解释：

该模式查找'#start gene'并捕获其背后事物的名称。 然后它会跳过所有内容到第一个'[' ，捕获所有内容到下一个']'的所有文本。

要写入文件，您需要对捕获的数据进行一些后处理，因为其中包含行拆分和 # 符号。

Answer 2

您可以使用正则表达式（模块re ）。 您必须捕获# protein sequence = [之后的所有文本

试试这段代码（这才刚刚开始）：

import re
regex = r"^# protein sequence = [([A-Z]+)$"
l = re.findall(regex, content_file, re.M)