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Viewing changes to scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
 
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#!/usr/bin/env perl
 
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# $Id: bp_seqfeature_gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $
 
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# AUTHOR: malcolm.cook@stowers-institute.org
 
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use strict;
 
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use Getopt::Long;
 
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use File::Spec;
 
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use Bio::DB::SeqFeature::Store;
 
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#use Carp::Always;
 
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my $DSN;
 
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my $ADAPTOR;
 
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my $VERBOSE  = 1;
 
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my $USER     = '';
 
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my $PASS     = '';
 
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my @gff3opt;
 
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GetOptions(
 
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           'dsn=s'       => \$DSN,
 
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           'adaptor=s'   => \$ADAPTOR,
 
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           'user=s'      => \$USER,
 
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           'password=s'  => \$PASS,
 
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           'gff3opt=i{,}'    => \@gff3opt,
 
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          ) || die <<END;
 
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Usage: $0 [options] -- [WHICH FEATURES]
 
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  output GFF3 for selected database features
 
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  Options:
 
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          -d --dsn        The database name ($DSN)
 
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          -a --adaptor    The storage adaptor to use ($ADAPTOR)
 
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          -u --user       User to connect to database as
 
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          -p --password   Password to use to connect to database
 
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          -g --gff3opt    flag options to gff3_string (i.e.: pass -gffopt 1 to recurse)
 
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         WHICH FEATURES: any remaining options after '--' will select
 
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         a subset of features. The arguments are identical to those
 
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         accepted by Bio::DB::SeqFeature::Store->features().
 
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END
 
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$ADAPTOR     ||= 'DBI::mysql';
 
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$DSN         ||= $ADAPTOR eq 'DBI::mysql' ? "mysql_read_default_file=$ENV{HOME}/.my.cnf" : '';
 
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my $store = Bio::DB::SeqFeature::Store->new(
 
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                                            -dsn     => $DSN,
 
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                                            -adaptor => $ADAPTOR,
 
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                                            -user    => $USER,
 
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                                            -pass    => $PASS,
 
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                                           )
 
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  or die "Couldn't create connection to the database";
 
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# on signals, give objects a chance to call their DESTROY methods
 
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$SIG{TERM} = $SIG{INT} = sub {   undef $store; die "Aborted..."; };
 
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my $seq_stream = $store->get_seq_stream(@ARGV)  or die "failed to get_seq_stream(@ARGV)"; 
 
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while (my $seq = $seq_stream->next_seq) {
 
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  print $seq->gff3_string(@gff3opt) . "\n";
 
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}
 
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exit 0;