Re: Bug in Bio::Phenotype::OMIM::OMIMparser

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Re: Bug in Bio::Phenotype::OMIM::OMIMparser

Fields, Christopher J
Peng,

Please post questions to the main BioPerl list (cc'd), and bug reports to our github tracker:

https://github.com/bioperl/bioperl-live/issues

After the bug is submitted we'll have a look but realize this is an open source project, and our time is pretty constrained.  In the meantime if you have time to dive in and make a suggested fix we'll be more than happy to accept it (patches are welcome but github pull requests are even better).

Chris

Sent from my iPhone

> On Mar 8, 2015, at 12:21 AM, Peng Yu <[hidden email]> wrote:
>
> Hi Chris,
>
> Bio::Phenotype::OMIM::OMIMparser can not process title with multiple
> lines correctly. See the following test case. Would you please fix it?
> Thanks.
>
> ~$ cat main.pl
> #!/usr/bin/env perl
>
> use strict;
> use warnings;
>
> use Bio::Phenotype::OMIM::OMIMparser;
> my $omim_parser = Bio::Phenotype::OMIM::OMIMparser->new(
>  -omimtext => '/dev/stdin' #$ARGV[0]
> );
>
> while(my $omim_entry = $omim_parser->next_phenotype()) {
>  print $omim_entry->title(), "\n";
> }
> ~$ cat main.sh
> #!/usr/bin/env bash
>
> (
> echo '*RECORD*'
> echo '*FIELD* NO'
> echo '616192'
> echo '*FIELD* TI'
> echo '#616192 ATAXIA, COMBINED CEREBELLAR AND PERIPHERAL, WITH HEARING LOSS AND'
> echo 'DIABETES MELLITUS; ACPHD'
> ) | ./main.pl
>
> ~/linux/test/perl/library/Bio/Phenotype/OMIM/OMIMparser/new/next_phenotype/title$
> ./main.sh
> #616192 ATAXIA, COMBINED CEREBELLAR AND PERIPHERAL, WITH HEARING LOSS AND
>
> --
> Regards,
> Peng

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