Replacing text in one file with text from another file

Question

I sequence headers in one file (eg, 'file1.fasta') that need to change to the corresponding headers from another file (eg, 'file2.fasta'). Notes: 1) Even though file1.fasta has some sequences reverse complemented from file2.fasta, I want to leave the sequences unmodified. 2) The file1.fasta sequences came from different sources, which means the headers display various formats; I'm targeting just a couple formats for modification.

Here is example of file2.fasta headers:

>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

Example of all the various header formats in file1.fasta (those targeted for modification are the first two headers):

>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

The last two are similar to those targeted, but have an extra underscore and a letter. These need to remain unmodified. Any headers that start with >uce and >ENSOFAS should be left alone. The new modified file1.fasta file should then look like:

>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

I have a python script someone provided that I used for a similar situation (but for differently formatted headers). I'm not familiar with python language, and curious if there is a way this script could be modified for this new purpose.

#!/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

If I understand now what you need it is just the following:

#!/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()