Perl: Split Loop for a Large txt File

Question

I am trying to split the contents of a txt file to extract relevant information using perl, but I can't seem to format my split statement correctly. A line of the file looks like this:

1.8|8|28|98|1pter-p22.1|SAI1, MTS1, TFS1|C|Suppression of anchorage independence-1 (malignant transformation suppression-1)|154280|S, H|||4(Tfs1)|

and my split statement looks like this:

my $file;
my $important;
my $line;
my @info;
foreach $line (@OMIMFile) {
my ($noSystem, $month, $day, $year, $cytoLoc, $geneSymb
    , $geneStat, $title, $mimNo, $method, $comment, $disorder
    , $mousCorr, $ref) = split ("|", $line);
    $important = $geneSymb.":".$disorder;
    push @info, $important if ($geneStat =~ /C/i);
}

I would like each line of @info to be the combination of $geneSymb and $disorder separated by a colon, but currently a print of @info returns nothing and $important returns an output like this:

|:||:|2:7|:|1:||:|0:||:|0:|1:85:|7:|9:01:37:93:93:93:92:71: .....

Where am I going wrong here?

Thanks in advance!

You forgot to escape pipe: \|. Also it should be a regex: /\|/. — TLP
– TLP, Commented Feb 7, 2014 at 13:38

user1126070 · Accepted Answer · 2014-02-07 13:40:51Z

1

Here is a fix.

Some of your variables was not local.

my $file;
my @info;
foreach my $line (@OMIMFile) {
my ($noSystem, $month, $day, $year, $cytoLoc, $geneSymb
    , $geneStat, $title, $mimNo, $method, $comment, $disorder
    , $mousCorr, $ref) = split (/\|/, $line);
    my $important = $geneSymb.":".$disorder;
    push @info, $important if ($geneStat =~ /C/i);
}

answered Feb 7, 2014 at 13:40

user1126070

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Comments

Borodin · Accepted Answer · 2014-02-07 13:48:13Z

0

This would be a lot neater using hash slices:

my @fields = qw/ noSystem month day year cytoLoc geneSymb geneStat title mimNo method comment disorder mousCorr ref /;
my @info;

for (@OMIMFile) {
  my %line;
  @line{@fields} = split /\|/;
  my $important = join ':', @line{ qw/ geneSymb disorder / };
  push @info, $important if $line{geneStat} =~ /C/i
}

answered Feb 7, 2014 at 13:48

Borodin

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