Question: seperate partial cds from complete cds
0
gravatar for Bulbul Ahmed
2.0 years ago by
Bulbul Ahmed20
United States
Bulbul Ahmed20 wrote:

I used the below perl script to remove out the partial cds, but its not working correctly and i am getting a blank output file. Can any body find out the the mistake and kindly correct it.

use strict;
use warnings;
open (fh, '<C:\Users\bulbul\Desktop\New folder\Unigene.transdecoder.cds.txt') or die "file not found,$!";
open (out, ">bulbul.txt");
while (my $line = "Unigene.transdecoder.cds.txt") {
    chomp $line;
    print "processing $line\n";
    my ($id, $rna_sq) = split(/\s+/, $line);

    while ($rna_sq =~ /atg/g) {

        my $start = pos($rna_sq) - 3; 

          last $rna_sq =~ /tga|taa|tag/g;

        my $stop    = pos($rna_sq);
        my $genelen = $stop - $start;

        my $gene    = substr($rna_sq, $start, $genelen);
        print "\t" . join(' ', $id, $start+1, $stop, $gene, $genelen) . "\n";
    }
}
rna-seq gene perl • 791 views
ADD COMMENTlink modified 2.0 years ago by RamRS23k • written 2.0 years ago by Bulbul Ahmed20

As an aside, since you're using Windows, you might want to ensure you're processing line breaks accurately. Newline characters are \r\n in Windows, and your input file or your output file might have different newline characters.

ADD REPLYlink written 2.0 years ago by RamRS23k

Still not working sir

ADD REPLYlink written 2.0 years ago by Bulbul Ahmed20
0
gravatar for RamRS
2.0 years ago by
RamRS23k
Houston, TX
RamRS23k wrote:

When you have a file handle, the while should be while(<fh>), not what you've used. Can you change that and see if it works?

ADD COMMENTlink written 2.0 years ago by RamRS23k
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