[Bioperl-l] <no subject>

[Stefan Kirov]

Sean,
I think this is the gene2xml converter. Try to run in it from command 
line and if you see an error parsing the resulting file let me know.
Stefan

Sean Davis wrote:

>#!/usr/bin/perl
>use strict;
>
>use Bio::ASN1::EntrezGene;
>use YAML;
>my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -I
>Homo_sapiens.ags.gz -c -x -b | ");
>
>while (my $res = $parser->next_seq) {
>  print "#######################################################\n";
>#  print Dump($res) . "\n";
>}
>
>Output is:
>#######################################################
>[NULL_Caption] FATAL ERROR: Input
>Entrezgene-Set.E.track-info.update-date
>Unable to match element in track-info.
>[NULL_Caption] FATAL ERROR: NULL value passed to object loader for
>Entrezgene
>[NULL_Caption] FATAL ERROR: Input
>Entrezgene-Set.E.track-info.update-date
>element status out of order in SEQUENCE Gene-track
>#######################################################
>#######################################################
>
>Is this a known issue, or a change in format from NCBI, or something else?
>
>Thanks,
>Sean
>
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