mmfunc.pl

#!/usr/bin/env perl
use strict;
use warnings;

# Daniel S. Standage <daniel.standage@gmail.com>
# Input:  sequences cleaned up and annotated by mRNAmarkup
# Output: each sequence ID along with its annotation, if any

my $usage = "perl $0 < cln-seqs.fas > seqids-and-funcs.txt";
while(<STDIN>)
{
  next unless(m/^>/);
  my($seqid) = m/^>(PdomTSAr1\.1-\d+)/;
  my $func = "NA";
  if(m/potential fusion transcript/)
  {
    $func = "potential fusion transcript";
  }
  elsif(m/matches \d+ \((.+)\)/)
  {
    $func = $1;
  }
  print "$seqid\t$func\n";
}