Re^4: An overlapping regex capture

Okay, I fixed up the items you suggested I should, and so my script is looking like this:

#!/usr/bin/perl 
use strict;
use warnings;


open my $fh, '<',"human_hg19_circRNAs_putative_spliced_sequence.fa",or
+ die $!;

my %id2seq;

    while(<$fh>){
        my $id = '';
        chomp;
        if($_ =~ /^>(.+)/){
            $id = $1;
        }else{
            $id2seq{$id} .= $_;
        }
    }

 

    foreach my $id (keys %id2seq){
        my $filename = (split /\|/, $id)[0];
        open  my $out_fh, '>>', "$filename" or die $!; 
        print $out_fh ">".$id."\n",$id2seq{$id}, "\n";
        close $out_fh;
    }


close $fh;
[download]

How do I integrate the value I've split and extracted into the naming of the file, because it's stating that it's uninitialised?

Although, I thought that it was clearly initialised/defined here:

  my $filename = (split /\|/, $id)[0];
        open  my $out_fh, '>>', "$filename" or die $!;
[download]

Or maybe I'm just misunderstanding the scope? Where do I place the $filename in the loop?

Pete.

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Re^5: An overlapping regex capture by poj (Abbot) on Jun 22, 2017 at 15:33 UTC
The problem is earlier where `$id` is set for the `>` lines but then cleared on the subsequent sequence lines `while(<$fh>){ my $id = ''; chomp; if ($_ =~ /^>(.+)/){ $id = $1; } else { $id2seq{$id} .= $_; } }` [download] Try `#!/usr/bin/perl use strict; use warnings; my $id; my %id2seq; my $infile = 'human_hg19_circRNAs_putative_spliced_sequence.fa'; open my $fh,'<',$infile or die "Could not open $infile : $!"; while (<$fh>){ if ( /^>(.+)/ ){ $id = (split /\\|/, $1)[0]; } $id2seq{$id} .= $_; } foreach my $id (keys %id2seq){ my $filename = $id.'.fa'; print "Creating $filename\n"; open my $out_fh,'>', $filename or die "Could not open $filename : $!"; print $out_fh $id2seq{$id}; close $out_fh; } close $fh;` [download] poj	[reply] [d/l] [select]
Re^5: An overlapping regex capture by 1nickt (Canon) on Jun 22, 2017 at 12:01 UTC
Did you try printing the values of your variables as I suggested? The way forward always starts with a minimal test.	[reply]
Re^6: An overlapping regex capture by Peter Keystrokes (Beadle) on Jun 22, 2017 at 18:17 UTC
Yes, I tried it and got the following: ID: at seqextractor.pl line 23, <$fh> line 130. Segments: $VAR1 = []; From the using the following `foreach my $id (keys %id2seq){ warn "ID: $id"; my @segments = split /\\|/, $id; warn "Segments: " . Dumper \@segments; my $filename = $segments[0]; }` [download] Does it mean that the array is empty?	[reply] [d/l]
Re^7: An overlapping regex capture by 1nickt (Canon) on Jun 22, 2017 at 21:24 UTC
Yes, that's right. And can you also see why the array is empty, from your debug statements? The way forward always starts with a minimal test.	[reply]