not used

modules/Bio/EnsEMBL/Utils/igi_utils.pm

-# $Id$
-
-# 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;