shabird has asked for the wisdom of the Perl Monks concerning the following question:

Hello Monks! i have a file that look like this:

 LOCUS       PPI3_SYNY3               379 aa            linear   BCT 1
+3-NOV-2019
DEFINITION  RecName: Full=Putative thylakoid lumen peptidyl-prolyl cis
+-trans
            isomerase sll0408; Short=Putative thylakoid lumen PPIase; 
+AltName:
            Full=Putative thylakoid lumen rotamase; Flags: Precursor.
ACCESSION   Q55118
VERSION     Q55118.2
REFERENCE   1  (residues 1 to 379)
  AUTHORS   Kaneko,T., Sato,S., Kotani,H., Tanaka,A., Asamizu,E., Naka
+mura,Y.,
            Miyajima,N., Hirosawa,M., Sugiura,M., Sasamoto,S., Kimura,
+T.,
            Hosouchi,T., Matsuno,A., Muraki,A., Nakazaki,N., Naruo,K.,
            Okumura,S., Shimpo,S., Takeuchi,C., Wada,T., Watanabe,A.,
            Yamada,M., Yasuda,M. and Tabata,S.
    TITLE     Sequence analysis of the genome of the unicellular cyano
+bacterium
            Synechocystis sp. strain PCC6803. II. Sequence determinati
+on of the
            entire genome and assignment of potential protein-coding r
+egions
  JOURNAL   DNA Res. 3 (3), 109-136 (1996)
   PUBMED   8905231
  REMARK    NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].;
            STRAIN=PCC 6803 / Kazusa
REFERENCE   2  (residues 1 to 379)

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I want to extract only these information from the file "PPI3_SYNY3 " , "Putative thylakoid lumen peptidyl-prolyl cis-trans isomerase sll0408" and "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions" Here is my code where i am only able to extract the locus id from the file please help me here

 
open(GENBANK, "/Users/ale/Desktop/seq.gp.txt") or die; 

# Opening file results.txt in write mode with the help of ">" operator
+.
    open (FH, ">", "results.txt"); 

my $content = join("", <GENBANK>); 

close(GENBANK);
$content =~ /LOCUS\s+([A-Z0-9_]+)/; 
my $locus = $1;
$content =~ /DEFINITION\s+(\w+\W+);
my $acids = $1 ;

$content =~ /TITLE([a-z0-9+\s]+)/; 

my $aminoAcids = uc($1);
print(FH "$locus\n$acids\n$aminoAcids\n");

[download]

Replies are listed 'Best First'.
Re: advance Regex
by hippo (Archbishop) on Apr 28, 2020 at 12:49 UTC

    Your second match has no captures and your third only matches lowercase. Regex might not be the best option for parsing this format in a robust fashion. That said:

    #!/usr/bin/env perl 
use strict;
use warnings;
use Test::More tests => 3;

my $content = join '', <DATA>;

$content =~ /LOCUS\s+([A-Z0-9_]+)/;
my $locus = $1;
$content =~ /(Putative.*?);/s;
my $acids = $1;
$acids =~ s/\n\s+/ /g;
$content =~ /TITLE\s*(.*?)\n\s+JOURNAL/s;
my $aminoAcids = $1;
$aminoAcids =~ s/\n\s+/ /g;

is $locus, 'PPI3_SYNY3';
is $acids, 'Putative thylakoid lumen peptidyl-prolyl cis-trans isomera
+se sll0408';
is $aminoAcids, 'Sequence analysis of the genome of the unicellular cy
+anobacterium Synechocystis sp. strain PCC6803. II. Sequence determina
+tion of the entire genome and assignment of potential protein-coding 
+regions';
__DATA__
 LOCUS       PPI3_SYNY3               379 aa            linear   BCT 1
+3-NOV-2019
DEFINITION  RecName: Full=Putative thylakoid lumen peptidyl-prolyl cis
+-trans
            isomerase sll0408; Short=Putative thylakoid lumen PPIase; 
+AltName:
            Full=Putative thylakoid lumen rotamase; Flags: Precursor.
ACCESSION   Q55118
VERSION     Q55118.2
REFERENCE   1  (residues 1 to 379)
  AUTHORS   Kaneko,T., Sato,S., Kotani,H., Tanaka,A., Asamizu,E., Naka
+mura,Y.,
            Miyajima,N., Hirosawa,M., Sugiura,M., Sasamoto,S., Kimura,
+T.,
            Hosouchi,T., Matsuno,A., Muraki,A., Nakazaki,N., Naruo,K.,
            Okumura,S., Shimpo,S., Takeuchi,C., Wada,T., Watanabe,A.,
            Yamada,M., Yasuda,M. and Tabata,S.
    TITLE     Sequence analysis of the genome of the unicellular cyano
+bacterium
            Synechocystis sp. strain PCC6803. II. Sequence determinati
+on of the
            entire genome and assignment of potential protein-coding r
+egions
  JOURNAL   DNA Res. 3 (3), 109-136 (1996)
   PUBMED   8905231
  REMARK    NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].;
            STRAIN=PCC 6803 / Kazusa
REFERENCE   2  (residues 1 to 379)

    [download]
[reply]
[d/l]

      Works fantastic. but can you explain the second and third regex to me? it will be your huge favour on me. this one:

      $content =~ /(Putative.*?);/s;
my $acids = $1;
$acids =~ s/\n\s+/ /g;

      [download]

      and this one

      $content =~ /TITLE\s*(.*?)\n\s+JOURNAL/s;
my $aminoAcids = $1;
$aminoAcids =~ s/\n\s+/ /g;

      [download]
[reply]
[d/l]
[select]

        The first one says to capture everything from the first P of Putative up to but not including the first following semi-colon. Subsequently the whitespace is collapsed.

        The second one says to capture everything after "TITLE" and its trailing space(s) up to but not including a newline followed by whitespace followed by "JOURNAL" (which is the following key). Again, subsequently the whitespace is collapsed.

        Both of these require the /s modifier. See perldoc perlre for details of the modifiers. You can also fall back on YAPE::Regex::Explain for any regexen that you are having trouble understanding, although it doesn't include support for more modern features, alas.

[reply]
[d/l]

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