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Full Discussion: Perl to adjust coordinates based on repeat string
Top Forums Shell Programming and Scripting Perl to adjust coordinates based on repeat string Post 303021888 by Aia on Monday 20th of August 2018 12:18:52 AM
Old 08-20-2018
In case that it is useful.

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

my @fasta = ();
while(<>) {
    chomp;
    if(/^>/){
        range_match(\@fasta) if @fasta;
        @fasta = ();
        push @fasta, $_;
        next;
    }
    $fasta[1] .= $_;
}
range_match(\@fasta);

sub range_match {
    my $fref = shift;
    my ($header, $seq) = @{$fref};
    my ($mark, $beginning, $end) = split /[:-]/, (split/\s+/, $header)[1];

    while($seq =~ /[tT]{4}/g) {
        my $first = "@-" + 1;
        my $last = "@+";
        printf "%s %s:%s-%s\n", $&, $mark, ($beginning + $first), ($beginning + $last);
    }
}

Code:
$ ./read_fasta.pl fasta.file
tttt range=chr2:166911127-166911130
tttt range=chr2:166911142-166911145
TTTT range=chr2:166911173-166911176
TTTT range=chr2:166911221-166911224
tttt range=chr2:166911287-166911290

This User Gave Thanks to Aia For This Post:
cmccabe
 

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LEARN ABOUT DEBIAN

dch-repeat

DCH-REPEAT(1)						      General Commands Manual						     DCH-REPEAT(1)

NAME

       dch-repeat - repeats a changelog entry into an older release

SYNOPSIS

       dch-repeat --build-tree <PATH>
       dch-repeat --source-release <RELEASE>
       dch-repeat --target-release <RELEASE>
       dch-repeat --devel-release <RELEASE>
       dch-repeat --pocket <POCKET>
       dch-repeat -h

DESCRIPTION

       dch-repeat  is  used  to  repeat a changelog into an older release.  It expects that --build-tree is laid out with each Ubuntu release as a
       separate directory ("feisty", "edgy", etc).

       For example, if gimp had a security update prepared for Feisty in $TREE/feisty/gimp-2.2.13, running  dch-repeat	in  $TREE/edgy/gimp-2.2.13
       would pull in the latest changelog from the Feisty build.

OPTIONS

       Listed below are the command line options for dch-repeat:

       -h or --help
	      Display a help message and exit.

       --build-tree PATH
	      Base of build trees. Default is /scratch/ubuntu/build.

       -s or --source-release RELEASE
	      Which release to take changelog from.

       --target-release RELEASE
	      Which release to build into.

       --devel-release RELEASE
	      Which release is the development release.

       --pocket POCKET
	      Which pocket to use.

AUTHOR

       dch-repeat was written by Kees Cook <kees@ubuntu.com>.  This manual page was written by Jonathan Patrick Davies <jpds@ubuntu.com>.

       Both are released under the GNU General Public License, version 2.

SEE ALSO

       dch(1).

ubuntu-dev-tools						  10 August 2008						     DCH-REPEAT(1)
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