From fb255cd14790922835ec8041bba8d59b39131b40 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Fri, 9 Jan 2004 16:14:32 +0000
Subject: [PATCH] not used
---
modules/Bio/EnsEMBL/Utils/igi_utils.pm | 147 -------------------------
1 file changed, 147 deletions(-)
delete mode 100644 modules/Bio/EnsEMBL/Utils/igi_utils.pm
diff --git a/modules/Bio/EnsEMBL/Utils/igi_utils.pm b/modules/Bio/EnsEMBL/Utils/igi_utils.pm
deleted file mode 100644
index edd297350d..0000000000
--- a/modules/Bio/EnsEMBL/Utils/igi_utils.pm
+++ /dev/null
@@ -1,147 +0,0 @@
-# $Id$
-
-# some utils for the igi work
-# copyright EnsEMBL (http://www.ensembl.org)
-# Written by Philip lijnzaad@ebi.ac.uk
-
-package Bio::EnsEMBL::Utils::igi_utils;
-
-### put all the igi's found in the summary into one big hash and return
-### it. The keys are the igi_ids; the values are a (ref to the) list of
-### native ids
-sub read_igis_from_summary {
- my ($IN) = @_;
- my %bighash = undef;
-
- SUMMARY_LINE:
- while (<$IN>) {
- next SUMMARY_LINE if /^#/;
- next SUMMARY_LINE if /^\s*$/;
- chomp;
-
- my @fields = split "\t", $_;
- my ($seq_name, $source, $feature,
- $start, $end, $score,
- $strand, $phase, $group_field) = @fields;
- $feature = lc $feature;
-
- unless ($group_field) {
- warn("no group field: skipping : '$_'\n");
- next SUMMARY_LINE ;
- }
-
- # Extract the extra information from the final field of the GTF line.
- my ($igi, $gene_name, $native_ids, $transcript_id, $exon_num, $exon_id) =
- parse_group_field($group_field);
-
- unless ($igi) {
- warn("no igi; skipping: '$_'\n");
- }
-
- $big_hash{$igi} = $native_ids;
- } # while <$IN>
- return \%big_hash;
-} # read_igis_from_summary
-
-### put all the transcript_ids found in the summary into one big hash and
-### return it. Key is transcript id; value is the summed length of all its
-### features.
-sub read_transcript_ids_from_summary {
- my ($IN) = @_;
- my %bighash = undef;
-
- SUMMARY_LINE:
- while (<$IN>) {
- next SUMMARY_LINE if /^#/;
- next SUMMARY_LINE if /^\s*$/;
- chomp;
-
- my @fields = split "\t", $_;
- my ($seq_name, $source, $feature,
- $start, $end, $score,
- $strand, $phase, $group_field) = @fields;
- $feature = lc $feature;
-
- unless ($group_field) {
- warn("no group field: skipping : '$_'\n");
- next SUMMARY_LINE ;
- }
-
- # Extract the extra information from the final field of the GTF line.
- my ($igi, $gene_name, $native_ids, $transcript_ids, $exon_num, $exon_id) =
- parse_group_field($group_field);
-
- if (@$transcript_ids==0) {
- die("no transcript_ids; skipping: '$_'\n");
- }
-
- if (@$transcript_ids==0) {
- die("no transcript_ids: '$_'\n");
- }
-
- foreach my $tid ( @$transcript_ids ) {
- $big_hash{$tid} ++;
- }
-
- } # while <$IN>
- return \%big_hash;
-} # read_transcript_ids_from_summary
-
-
-# return a list of fields from a gtf file.
-# native_id and trancript_id are lists, since the
-# summary files usually contain more than one native id and transcript_id
-sub parse_group_field {
- my( $group_field ) = @_;
-
- my ($igi, $gene_name, @native_ids, @transcript_ids, $exon_num, $exon_id);
-
- # Parse the group field
- foreach my $tag_val (split /;/, $group_field) {
-
- # Trim trailing and leading spaces
- $tag_val =~ s/^\s+|\s+$//g;
-
- my($tag, $value) = split /\s+/, $tag_val, 2;
-
- # Remove quotes from the value
- $value =~ s/^"|"$//g;
- $tag = lc $tag;
-
- if ($tag eq 'igi_id') {
- $igi = $value;
- }
- elsif ($tag eq 'gene_name') {
- $gene_name = $value;
- }
- elsif ($tag eq 'gene_id') {
- push @native_ids, $value;
- }
- elsif ($tag eq 'transcript_id') {
- push @transcript_ids, $value;
- }
- elsif ($tag eq 'exon_number') {
- $exon_num = $value;
- }
- elsif ($tag eq 'exon_id') {
- $exon_id = $value;
- }
- else {
- #warn "Ignoring group field element: '$tag_val'\n";
- }
- }
- return($igi, $gene_name, \@native_ids, \@transcript_ids, $exon_num, $exon_id);
-} # parse_group_field
-
-
-### sorts igi3_5 igi3_10 on the basis of the numbers. call as :
-###
-### sort { Bio::EnsEMBL::Utils::igi_utils::by_igi_number($a, $b) } @igis;
-###
-###
-sub by_igi_number {
- my ($aa, $bb) = (substr($_[0],5), substr($_[1],5));
- $aa <=> $bb;
-}
-
-1;
--
GitLab