A script to add TSDs to sequences in a FASTA file

#!/usr/bin/perl -w

#

# A script to add TSDs (from another FASTA file that is a sole argument of the command, 

# wildcards allowed) to sequences in a FASTA file (input, output).

#

# Author: Matej Lexa

# Date: 2019/11/19

#

$sequence = "";

$files = $ARGV[0];

while($_=<STDIN>){

  if($_=~/^>/){

    if($sequence ne ""){

      $tsd = `grep -v \"^>\" $files \| grep . \| shuf \| head -1 \| egrep -o \"[A-Za-z]+\$\" \| cat`;

      chop($tsd);

      print "$tsd$sequence$tsd\n\n";

    }

    $sequence = "";

    print $_;

  } else {

    chop($_);

    $sequence .= uc($_);

  }

}

#$tsd = `grep -v \"^>\" $files \| grep .\| shuf \| head -1 \| egrep -o \"[A-Za-z]+\$\" \| cat`;

#chop($tsd);

print "$tsd$sequence$tsd\n\n";

exit(1);