[Bioperl-l] <no subject>

[Mingyi Liu]

The output error message should be gene2xml's error message 
(Bio::ASN1::EntrezGene does not depends on other modules and does not 
produce such error message).  It's either gene2xml did not work as 
called or the way the pipe was opened caused trouble.  I'll investigated 
it further.

Mingyi

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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