crufty

scripts/Analysis/genomic_cdna_test

-#!/usr/local/bin/perl
-
-use strict;
-
-=head1 NAME
-
-
-=head1 SYNOPSIS
-
-
-=head1 DESCRIPTION
-
-
-=cut
-
-use Bio::EnsEMBL::Analysis::PairAlign;
-
-use Bio::EnsEMBL::SeqFeature;
-use Bio::EnsEMBL::FeaturePair;
-use Bio::SeqFeature::FeaturePair;
-
-use Getopt::Long;
-
-# Takes an msp file and a series of coords to convert as input
-
-my $file  = shift;
-
-my @coords = @ARGV;
-
-open(IN,"<$file") || die "Can't open file $file";
-my $infh = \*IN;
-
-my %pairs;
- 
-while (my $line = <$infh>) {
-    my $pair = read_FeaturePair($line);
-    my $id    = $pair->primary_tag;
-	    
-    if (!defined($pairs{$id})) {
-	$pairs{$id} = new Bio::EnsEMBL::Analysis::PairAlign;
-    }
-
-    $pairs{$id}->addFeaturePair($pair);
-}
-
-foreach my $key (keys %pairs) {
-
-    foreach my $pair1 ($pairs{$key}->eachFeaturePair) {
-	my $pair2  = $pair1->feature2;
-;
-	print($pair1->start . " " . 
-	      $pair1->end   . " " . 
-	      $pair2->start . " " . 
-	      $pair2->end   . "\n");
-
-    }
-    foreach my $c (@coords) {
-	my $out = $pairs{$key}->genomic2cDNA($c);
-	print("Genomic $c - cDNA $out\n");
-    }
-	
-}
-
-
-sub read_FeaturePair {
-    my ($line) = @_;
-    chomp($line);
-
-    my ($score,$pid,$qstart,$qend,$id1,$hstart,$hend,$id2,$desc) = split(' ',$line,9);
-
-    my $strand1 = 1;
-    my $strand2 = 1;
-
-    if ($qstart > $qend ) {
-	my $tmp    = $qend;
-  	   $qend   = $qstart;
-	   $qstart = $tmp;
-
-	$strand1 = -1;}
-
-    if ($hstart > $hend ) {
-
-	my $tmp    = $hend;
-	   $hend   = $hstart;
-	   $hstart = $tmp;
-
-	$strand2 = -1;
-    }
-
-    my $sf1 = new Bio::EnsEMBL::SeqFeature(-start  => $qstart,
-					   -end    => $qend,
-					   -strand => $strand1,
-					   -primary_tag => $id1);
-
-
-    my $sf2 = new Bio::EnsEMBL::SeqFeature(-start  => $hstart,
-					   -end    => $hend,
-					   -strand => $strand2,
-					   -primary_tag => $id2);
-
-
-    my $fp = new Bio::EnsEMBL::FeaturePair(-feature1 => $sf1,
-					   -feature2 => $sf2,
-					   );
-
-    return ($fp);
-}
-
-