Question

我将标题排在一个文件中（例如，＆＃39; file1.fasta＆＃39;），需要更改为另一个文件中的相应标题（例如，＆＃39; file2.fasta＆＃39;）。注意：1）即使file1.fasta有一些从file2.fasta反向补充的序列，我想保留序列不被修改。 2）file1.fasta序列来自不同的来源，这意味着标题显示各种格式;我只针对几种格式进行修改。

以下是file2.fasta标题的示例：

>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中所有各种标题格式的示例（目标是修改的是前两个标题）：

>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

最后两个与目标相似，但有一个额外的下划线和一个字母。这些需要保持不变。任何以>uce和>ENSOFAS开头的标头都应该保持不变。新修改的file1.fasta文件应如下所示：

>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

我有一个python脚本提供了我用于类似情况（但对于不同格式的标题）。我不熟悉python语言，并且好奇是否可以为这个新目的修改此脚本。

#!/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

如果我现在明白你的需要，那就是以下内容：

#!/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()

用另一个文件

1 个答案: