使用另一個文件中的文本替換一個文件中的文本

Question

我需要從另一個文件（例如，'file2.fasta'）更改爲相應頭文件的一個文件（例如'file1.fasta'）中排序標頭。注意：1）儘管file1.fasta有一些從file2.fasta反向補充的序列，但我希望不修改序列。 2）file1.fasta序列來自不同的來源，這意味着標題顯示各種格式;我針對的只是幾種格式的修改。

下面是示例file2.fasta報頭：

實施例的 所有各種報頭格式在file1.fasta

>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 

（那些針對修改是前兩個報頭）：

>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 

最後兩個與目標類似，但有一個額外的下劃線和一個字母。這些需要保持不變。任何以>uce和>ENSOFAS開頭的標題都應該單獨保留。然後，新修改的file1.fasta文件應該是這樣的：

>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python腳本有人前提是我用了類似的情況（但對於不同格式的頭）。我對python語言並不熟悉，並且好奇這個腳本是否可以修改用於這個新目的。

#!/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

如果我現在明白你需要它只是下面的內容：

#!/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()