用另一個文件中的文本替換一個文件中的文本

Question

我在一個文件（例如，“ file1.fasta”）中的標頭排序，該標頭需要從另一個文件（例如，“ file2.fasta”）更改為相應的標頭。 注意：1）即使file1.fasta的某些序列與file2.fasta的序列相反，我仍希望這些序列保持不變。 2）file1.fasta序列來自不同的來源，這意味着標頭顯示各種格式； 我只針對幾種格式進行修改。

這是file2.fasta標頭的示例：

>OFAS009268-RA-EXON07 |design:coreoidea-v1,designer:forthman,probes-locus:OFAS009268-RA-EXON07,probes-probe:,probes-source:Clavigralla_tomentosicollis_gi_512427643_gb_GAJX01006991.1
CATTGCAGCAACTAACAGAGTTGATATATTAGATCCAGCCCTTCTCCGATCAGGCAGGCTAGACAGAAAAATTGAATTTCCTCATCCAAATGAAGATGCCCGTGCTCGAATTATGCAAAT
>OFAS016134-RA-EXON02 |design:coreoidea-v1,designer:forthman,probes-locus:OFAS016134-RA-EXON02,probes-probe:,probes-source:Anasa_tristis_comp3229_c0_seq1
AGGGCTTGTGATTCCCTTGAGCACATCGCAAGCCTCTGTTCTAGACAAAACATTCCACATTTGGTCAATAATGCTTTTGGTTTGCAAAGTGCACGTCTCATGCATTTAATTCAAGAGGCT

file1.fasta中所有各種標頭格式的示例（用於修改的標頭是前兩個標頭）：

>Clavigralla_tomentosicollis_gi_512427643_gb_GAJX01006991.1_103_rc
CATTGCAGCAACTAACAGAGTTGATATATTAGATCCAGCCCTTCTCCGATCAGGCAGGCTAGACAGAAAAATTGAATTTCCTCATCCAAATGAAGATGCCCGTGCTCGAATTATGCAAAT
>Anasa_tristis_comp3229_c0_seq1_0_rc
AGGGCTTGTGATTCCCTTGAGCACATCGCAAGCCTCTGTTCTAGACAAAACATTCCACATTTGGTCAATAATGCTTTTGGTTTGCAAAGTGCACGTCTCATGCATTTAATTCAAGAGGCT
>ENSOFAS009761_p2 |design:coreoidea-v1,designer:forthman,probes-locus:ENSOFAS009761,probes-probe:2,probes-source:Anoplocnemis_curvipes_contig5129
TTAAGAATCTCGAGAAAACCCCTCAGGATGATGAATTACTTGAAATATATGCTCTCTATAAACAAGCAACTGTAGGAGACTGTGACACAAGTAAGCCTGGGATGTTTGATTTCAAAGGGA1
>uce-3225_p7 |design:hemiptera-v1,designer:faircloth,probes-locus:uce-3225,probes-probe:7,probes-source:halhal1,probes-global-chromo:Scaffold629,probes-global-start:410155,probes-global-end:410275,probes-local-start:0,probes-local-end:120
AAATCCATCAAGAAATACCAACAACAACTTAAGGATGTCCAGACCGCACTCGAGGAAGAACAAAGAGCTAGGGATGATGCCCGAGAACAACTTGGTATTGCCGAAAGGCGAGCCAACGCT
>Anasa_tristis_comp8051_c0_seq1_A_0
ATCCTCCTGATTGGGCAGAAATTTTGAACCATTTTCGAGGGTCTGAACTTCAGAATTATTTTACAAAAATTTTGGAGGATGACCTTAAAGCCCTTATCAAGCCTCAGTATGTCGACCAAA
>Anasa_tristis_comp8051_c0_seq1_B_0
TAACGTCCTAGGTTAGGTTTCTGTTTACCAGCTAAAATCTTGAGGGCTGTAGACTTTCCAATGCCATTAGTTCCAACCAGACCTAAAACTTCTCCTGGTCTTGGAATTGGAAGTCTGTGG

后兩個與目標對象相似，但是下划線和字母后面有一個額外的下划線。 這些需要保持不變。 以>uce和>ENSOFAS開頭的任何標頭>ENSOFAS應該保留。 新修改的file1.fasta文件應如下所示：

>OFAS009268-RA-EXON07 |design:coreoidea-v1,designer:forthman,probes-locus:OFAS009268-RA-EXON07,probes-probe:,probes-source:Clavigralla_tomentosicollis_gi_512427643_gb_GAJX01006991.1_OFAS009268-RA-EXON07
CATTGCAGCAACTAACAGAGTTGATATATTAGATCCAGCCCTTCTCCGATCAGGCAGGCTAGACAGAAAAATTGAATTTCCTCATCCAAATGAAGATGCCCGTGCTCGAATTATGCAAAT
>OFAS016134-RA-EXON02 |design:coreoidea-v1,designer:forthman,probes-locus:OFAS016134-RA-EXON02,probes-probe:,probes-source:Anasa_tristis_comp3229_c0_seq1_OFAS016134-RA-EXON02
AGGGCTTGTGATTCCCTTGAGCACATCGCAAGCCTCTGTTCTAGACAAAACATTCCACATTTGGTCAATAATGCTTTTGGTTTGCAAAGTGCACGTCTCATGCATTTAATTCAAGAGGCT
>ENSOFAS009761_p2 |design:coreoidea-v1,designer:forthman,probes-locus:ENSOFAS009761,probes-probe:2,probes-source:Anoplocnemis_curvipes_contig5129
TTAAGAATCTCGAGAAAACCCCTCAGGATGATGAATTACTTGAAATATATGCTCTCTATAAACAAGCAACTGTAGGAGACTGTGACACAAGTAAGCCTGGGATGTTTGATTTCAAAGGGA1
>uce-3225_p7 |design:hemiptera-v1,designer:faircloth,probes-locus:uce-3225,probes-probe:7,probes-source:halhal1,probes-global-chromo:Scaffold629,probes-global-start:410155,probes-global-end:410275,probes-local-start:0,probes-local-end:120
AAATCCATCAAGAAATACCAACAACAACTTAAGGATGTCCAGACCGCACTCGAGGAAGAACAAAGAGCTAGGGATGATGCCCGAGAACAACTTGGTATTGCCGAAAGGCGAGCCAACGCT
>Anasa_tristis_comp8051_c0_seq1_A_0
ATCCTCCTGATTGGGCAGAAATTTTGAACCATTTTCGAGGGTCTGAACTTCAGAATTATTTTACAAAAATTTTGGAGGATGACCTTAAAGCCCTTATCAAGCCTCAGTATGTCGACCAAA
>Anasa_tristis_comp8051_c0_seq1_B_0
TAACGTCCTAGGTTAGGTTTCTGTTTACCAGCTAAAATCTTGAGGGCTGTAGACTTTCCAATGCCATTAGTTCCAACCAGACCTAAAACTTCTCCTGGTCTTGGAATTGGAAGTCTGTGG

我有一個有人提供的python腳本，用於類似情況（但格式不同的標頭）。 我不熟悉python語言，並且很好奇是否可以為此新目的修改此腳本。

#!/usr/bin/env python

import sys
import re

original_fn = sys.argv[1]
company_fn = sys.argv[2]

pattern = '(uce | ENSOFAS | _[AB]_[0-9]+$)'

map = {}

with open(original_fn, "r") as original_fh:
    for line in original_fh:
        if line.startswith('>'):
            try:
                 (k, v) = line.strip().split('|')
                 # remove trailing space from key
                 k = k[:-1]
                 map[k] = v
            except ValueError as err:
                 k = line.strip()
                 map[k] = None

with open(company_fn, "r") as company_fh:
    for line in company_fh:
        if line.startswith('>') and not re.search(pattern, line.strip()):
            try:
                (k, v) = line.strip().split('|')
                # remove trailing character from key
                k = k[:-1]
            except ValueError as err:
                k = line.strip()
            if k not in map:
                sys.stdout.write("%s\n" % (k))
            else:
                sys.stdout.write("%s |%s\n" % (k, map[k]))
        else:
            sys.stdout.write("%s" % (line))

Answer 1

如果我現在了解您所需要的，則僅是以下內容：

#!/usr/bin/env python

import sys

original_fn = sys.argv[1]
company_fn = sys.argv[2]

fpOriginal  =  open(original_fn, "r")

for lineCompany in open(company_fn, "r").readlines():
  if lineCompany.startswith('*'):
    sys.stdout.write( fpOriginal.readline() )
    fpOriginal.readline()
  else:
    sys.stdout.write( lineCompany )

fpOriginal.close()