Modyfing a Genbank file

Question

[matt81rd]

Hi i am trying to search through a file for a specific list of words. If one of those words if found i want to add a newline underneath and add this phrase \colour = 1 (I don't want to remove the orginal word i am searching for).

An extract of the file for context and format:

> LOCUS       contig_2_pilon_pilon 5558986 bp    DNA     linear   BCT
> 16-JUN-2020 DEFINITION  Escherichia coli O157:H7 strain (270078)
> ACCESSION    VERSION KEYWORDS    . SOURCE      Escherichia coli 270078
> ORGANISM  Escherichia coli 270078
>             Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
>             Escherichia. COMMENT     Annotated using prokka 1.14.6 from
>             https://github.com/tseemann/prokka. FEATURES             Location/Qualifiers
>      source          1..5558986
>                      /organism="Escherichia coli 270078"
>                      /mol_type="genomic DNA"
>                      /strain="strain"
>                      /db_xref="taxon:562"
>      CDS             61523..61744
>                      /gene="pspD"
>                      /locus_tag="JCCJNNLA_00057"
>                      /inference="ab initio prediction:Prodigal:002006"
>                      /inference="similar to AA sequence:RefSeq:EG10779-MONOMER"
>                      /codon_start=1
>                      /transl_table=11
>                      /product="peripheral inner membrane heat-shock protein"
>                      /translation="MNTRWQQAGQKVKPGFKLAGKLVLLTALRYGPAGVAGWAIKSVA
>                      RRPLKMLLAVALEPLLSRAANKLAQRYKR"

Here is one of the lists of words i am looking for throughout the file:

regulation_list=["anti-repressor","anti-termination","antirepressor","antitermination","antiterminator","anti-terminator","cold-shock","cold shock","heat-shock","heat shock","regulation","regulator","regulatory","helicase","antibiotic resistance","repressor","zinc","sensor","dipeptidase","deacetylase","5-dehydrogenase","glucosamine kinase","glucosamine-kinase","dna-binding","dna binding","methylase","sulfurtransferase","acetyltransferase","control","ATP-binding","ATP binding","Cro","Ren protein","CII","inhibitor","activator","derepression","protein Sxy","sensing","sensor","Tir chaperone","Tir-cytoskeleton","Tir cytoskeleton","Tir protein","EspD"]

As you can see that extract contains one of th ephrases i am looking for and i want to add a newline underneath with the phrase /colour = 1

Any help would be great!

[lieven.sterck]

if there are not too many you need to process you can open those kind of file(s) in a genome browser (apollo, artemis GenomeView, ... ) and change the color of the feature using the browser. afterwards you can then save the file again.

Answer 1

[JC]

Perl solution:

#!/usr/bin/perl

use strict;

use warnings;

my @regulation_list = ("anti-repressor","anti-termination","antirepressor","antitermination","antiterminator","anti-terminator","cold-shock","cold shock","heat-shock","heat shock","regulation","regulator","regulatory","helicase","antibiotic resistance","repressor","zinc","sensor","dipeptidase","deacetylase","5-dehydrogenase","glucosamine kinase","glucosamine-kinase","dna-binding","dna binding","methylase","sulfurtransferase","acetyltransferase","control","ATP-binding","ATP binding","Cro","Ren protein","CII","inhibitor","activator","derepression","protein Sxy","sensing","sensor","Tir chaperone","Tir-cytoskeleton","Tir cytoskeleton","Tir protein","EspD");

my $list_regex = join "|", @regulation_list;

while (<>) {
    print;
    if (m|(\s+)/product=.*($list_regex)|i) {
        my $pre = $1;
        print "$pre/colour = 1\n";
    }
}

testing it:

$ perl checkWords.pl < file.gbk
LOCUS       contig_2_pilon_pilon 5558986 bp    DNA     linear   BCT
16-JUN-2020 DEFINITION  Escherichia coli O157:H7 strain (270078)
ACCESSION    VERSION KEYWORDS    . SOURCE      Escherichia coli 270078
ORGANISM  Escherichia coli 270078
            Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
            Escherichia. COMMENT     Annotated using prokka 1.14.6 from
            https://github.com/tseemann/prokka. FEATURES             Location/Qualifiers
     source          1..5558986
                     /organism="Escherichia coli 270078"
                     /mol_type="genomic DNA"
                     /strain="strain"
                     /db_xref="taxon:562"
     CDS             61523..61744
                     /gene="pspD"
                     /locus_tag="JCCJNNLA_00057"
                     /inference="ab initio prediction:Prodigal:002006"
                     /inference="similar to AA sequence:RefSeq:EG10779-MONOMER"
                     /codon_start=1
                     /transl_table=11
                     /product="peripheral inner membrane heat-shock protein"
                     /colour = 1
                     /translation="MNTRWQQAGQKVKPGFKLAGKLVLLTALRYGPAGVAGWAIKSVA
                     RRPLKMLLAVALEPLLSRAANKLAQRYKR"