From c46eb26d8f81b1db188675aa6b7a82087a23b9ef Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Wed, 25 Feb 2004 11:16:47 +0000
Subject: [PATCH] crufty
---
scripts/Analysis/genomic_cdna_test | 109 -----------------------------
1 file changed, 109 deletions(-)
delete mode 100755 scripts/Analysis/genomic_cdna_test
diff --git a/scripts/Analysis/genomic_cdna_test b/scripts/Analysis/genomic_cdna_test
deleted file mode 100755
index ee44dab22f..0000000000
--- a/scripts/Analysis/genomic_cdna_test
+++ /dev/null
@@ -1,109 +0,0 @@
-#!/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);
-}
-
-
--
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