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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 OSX

repeat

textutil::repeat(n)				    Text and string utilities, macro processing 			       textutil::repeat(n)

__________________________________________________________________________________________________________________________________________________

NAME

       textutil::repeat - Procedures to repeat strings.

SYNOPSIS

       package require Tcl  8.2

       package require textutil::repeat  ?0.7?

       ::textutil::repeat::strRepeat text num

       ::textutil::repeat::blank num

_________________________________________________________________

DESCRIPTION

       The package textutil::repeat provides commands to generate long strings by repeating a shorter string many times.

       The complete set of procedures is described below.

       ::textutil::repeat::strRepeat text num
	      This  command returns a string containing the text repeated num times. The repetitions are joined without characters between them. A
	      value of num <= 0 causes the command to return an empty string.

	      Note: If the Tcl core the package is loaded in provides the command string repeat then this  command  will  be  implemented  in  its
	      terms, for maximum possible speed. Otherwise a fast implementation in Tcl will be used.

       ::textutil::repeat::blank num
	      A convenience command. Returns a string of num spaces.

BUGS, IDEAS, FEEDBACK
       This document, and the package it describes, will undoubtedly contain bugs and other problems.  Please report such in the category textutil
       of the Tcllib SF Trackers [http://sourceforge.net/tracker/?group_id=12883].  Please also report any ideas for enhancements you may have for
       either package and/or documentation.

SEE ALSO

       regexp(n), split(n), string(n)

KEYWORDS

       blanks, repetition, string

CATEGORY

       Text processing

textutil							       0.7.1						       textutil::repeat(n)
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