[Bioperl-l] genbank parsing of multiple 'function' tags within primary tag

[Frank Schwach]

I only had a quick look at your code, so maybe I'm missing something but
you are currently pushing all products of all CDSs into the same array,
i.e. you do not assign them to a datastructure that links a particular
CDS to a list of products. You then use the same index to print out a
locus from the @loci array and a product from @products, but the two
will not match up because you will have more products than loci.

Frank



On Thu, 2011-09-08 at 10:44 -0400, galeb abu-ali wrote:
> Hi,
> 
> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
> multiple tags within a primary tag.  E.g., when there are several 'function'
> tag-values within a 'CDS' primary tag, I don't know how to link those
> 'function' tag-values to a particular 'locus_tag'.  As parsed values are
> returned as a list, I tried creating an array of hashes, where the hash-key
> is 'locus_tag' and hash-values are multiple 'function' tags, but am failing
> miserably.  Pasted below is what I managed so far.  At your convenience,
> please advise.
> 
> thanks!
> 
> galeb
> 
> #!/usr/local/bin/perl
> # parse_gbk.pl
> # gsa 09042011
> # script to parse out features from gbk
> #
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Customizing_Sequence_Object_Construction
> 
> use strict; use warnings;
> use Bio::SeqIO;
> 
> my @loci;
> my @seqs;
> my @directions;
> my @start_coords;
> my @end_coords;
> my @genes;
> my @products;
> my @notes;
> my @functions;
> my %functions;
> 
> my $gb_file = shift;
> my $seqio_obj = Bio::SeqIO->new(-file => $gb_file );
> my $seq_obj = $seqio_obj->next_seq;
> 
> for my $feat_obj ( $seq_obj->get_SeqFeatures ) {
>     if ( $feat_obj->primary_tag eq ( 'gene' ) ) {
>                 if ($feat_obj->has_tag( 'locus_tag' ) ) {
>                 push ( @seqs, $feat_obj->seq->seq ); #collect sequences
>                     for my $val ( $feat_obj->get_tag_values( 'locus_tag' ) )
> {
>                             push ( @loci, $val ); # locus_tags
>             }
>         }
>                 if ( $feat_obj->has_tag( 'gene' ) ) {
>                            for my $val ( $feat_obj->get_tag_values( 'gene' )
> ) {
>                             push ( @genes, $val ); # gene names
>                         }
>                 }
>                 else {
>                     push ( @genes, "" ); # if gene names are absent, leave
> empty
>         }
>         if ( $feat_obj->location->isa( 'Bio::Location::Simple' ) ) { # gene
> coordinates
>             for my $location ( $feat_obj->location ) {
>                 push ( @start_coords, $location->start );
>                 push ( @end_coords, $location->end );
>                 if ( $location->strand == -1 ) {
>                     push ( @directions, "reverse" );
>                 }
>                 else {
>                     push ( @directions, "forward" );
>                 }
>             }
>         }
>     }
>     # gene products, notes, functions
>     if ( $feat_obj->primary_tag eq ( 'CDS' ) || $feat_obj->primary_tag eq (
> 'misc_feature' ) || $feat_obj->primary_tag eq ( 'ncRNA' ) ||
> $feat_obj->primary_tag eq ( 'rRNA' ) || $feat_obj->primary_tag eq ( 'tRNA' )
> || $feat_obj->primary_tag eq ( 'misc_RNA' ) ) {
>         if ( $feat_obj->has_tag( 'product' ) ) {
>             for my $product ( $feat_obj->get_tag_values( 'product' ) ) {
>                 push ( @products, $product );
>             }
>         }
>         else {
>             push ( @products, "" );
>         }
>         if ( $feat_obj->has_tag( 'note' ) ) {
>             for my $note ( $feat_obj->get_tag_values( 'note' ) ) {
>                 push ( @notes, $note );
>             }
>         }
>         else {
>             push ( @notes, "" );
>         }
>         if ( $feat_obj->has_tag( 'function' ) ) {
>             for my $function ( $feat_obj->get_tag_values( 'function' ) ) {
>                 push ( @functions, $function );
>             }
>         }
>         else {
>             push ( @functions, "" );
>         }
> 
>     }
> }
> 
> print
> "locus\tgene_name\tstart_nt\tend_nt\tlength_nt\tdirection\tproduct\tnote\tfunction\tsequence_nt\n";
> # header
> 
> for ( my $elem = 0; $elem < scalar @loci; ++$elem ) {
>     print $loci[$elem], "\t",$genes[$elem], "\t", $start_coords[$elem],
> "\t", $end_coords[$elem], "\t", length( $seqs[$elem] ), "\t",
> $directions[$elem], "\t", $products[$elem], "\t", $notes[$elem], "\t",
> $functions[$elem], "\t", $seqs[$elem], "\n";
> }
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