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#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
# a gff file looks like this:
#<seqname> <source> <feature> <start> <end> <score> <strand> <frame> [attributes] [comments]
sub generateGff {
my $data=shift;
my $returnstring = "";
$returnstring .= "$$data{'seqname'}\t";
$returnstring .= "$$data{'source'}\t";
$returnstring .= "$$data{'feature'}\t";
$returnstring .= "$$data{'start'}\t";
$returnstring .= "$$data{'end'}\t";
$returnstring .= "$$data{'score'}\t";
$returnstring .= "$$data{'strand'}\t";
$returnstring .= "$$data{'frame'}\t";
$returnstring .= "$$data{'additional'}";
return $returnstring;
}
#this sub takes 3 parameters,
# $fastastring: the fasta string we want to parse,
# $data: a reference to a hash where we save all the results in
# $radius: we are calculating the start and the end values with this variable.
sub parseFasta {
my $fastaString=shift;
my $data=shift;
my $radius=shift;
if ($fastaString =~ m/^(.*)-([\d]*)_([\+-])\s([\d]*)\stranscripts:\s([^,]*).*$/) {
$$data{'seqname'} = $1;
$$data{'source'} = "PASA";
$$data{'feature'} = "tts";
$$data{'start'} = $2-$radius;
$$data{'end'} = $2+$radius;
$$data{'score'} ="$4";
$$data{'strand'} ="$3";
$$data{'frame'} =".";
my $temp=$5;
if ($temp =~ m/(gi\|\d+\|).*/) {
$temp = $1;
}
$$data{'additional'} ="pri=4;EST=$temp;src=E";
return $data;
}
else {
return undef;
}
}
sub main {
#carries the information from one format to the other
my %shuttle=();
#setting the USAGE variable
my $USAGE="USAGE: pasapolyA2hints.pl <PASA-Output file in fasta-format> [--radius=integer]\n";
my $rad=5;
my $pasapolyAfile="";
GetOptions("radius:i"=> \$rad);
if (scalar(@ARGV) < 1) {
die $USAGE;
}
else {
$pasapolyAfile=$ARGV[0];
open(FASTA, "<$pasapolyAfile") || die "Couldn't open $ARGV[0]\n";
$/="\n>";
while(<FASTA>) {
/[>]*(.*)\n/;
my $temp = $1;
chomp($temp);
&parseFasta($temp,\%shuttle,$rad);
print(&generateGff(\%shuttle),"\n");
}
}
}
&main;
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