Re: Can you make this code shorter and/or quicker as well?

Perhaps the following will be helpful:

use strict;
use warnings;

local $/ = '>';

while (<>) {
    chomp;
    my ( $id, $seq ) = /(.+?\n)(.+)/s or next;
    $seq =~ s/\s+//g;
    print ">$id$seq\n";
}
[download]

Command-line usage: perl script.pl fastaIn [>fastaOut]

The last, optional parameter directs output to a file.

Comment on Re: Can you make this code shorter and/or quicker as well? Select or Download Code

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Re^2: Can you make this code shorter and/or quicker as well? by Anonymous Monk on Feb 25, 2014 at 00:26 UTC
How can I put it in a sub-routine that I could use inline my script? Something like: `sub extract_query_data($file);` [download]	[reply] [d/l]
Re^3: Can you make this code shorter and/or quicker as well? by Anonymous Monk on Feb 25, 2014 at 00:27 UTC
Sorry, I meant: `extract_query_data($file);` [download]	[reply] [d/l]
Re^4: Can you make this code shorter and/or quicker as well? by Kenosis (Priest) on Feb 25, 2014 at 00:36 UTC
Here's one option: `use strict; use warnings; for my $fastaRec ( extract_query_data('fastaFile.fa') ) { print $fastaRec, "\n"; } sub extract_query_data { my ($file) = @_; my @arr; local $/ = '>'; open my $fh, '<', $file or die $!; while (<$fh>) { chomp; my ( $id, $seq ) = /(.+?\n)(.+)/s or next; $seq =~ s/\s+//g; push @arr, ">$id$seq"; } close $fh; return @arr; }` [download] You'll note that the subroutine returns an array of fasta records.	[reply] [d/l]
Re^5: Can you make this code shorter and/or quicker as well? by Anonymous Monk on Feb 25, 2014 at 00:37 UTC


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