/usr/bin/bp_seqfeature_gff3 is in bioperl 1.6.923-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 | #!/usr/bin/env perl
# AUTHOR: malcolm.cook@stowers-institute.org
use strict;
use warnings;
use Carp;
use Getopt::Long;
use File::Spec;
use Bio::DB::SeqFeature::Store;
#use Carp::Always;
my $DSN;
my $ADAPTOR;
my $VERBOSE = 1;
my $USER = '';
my $PASS = '';
my @gff3opt;
GetOptions(
'dsn=s' => \$DSN,
'adaptor=s' => \$ADAPTOR,
'user=s' => \$USER,
'password=s' => \$PASS,
'gff3opt=i{,}' => \@gff3opt,
) || die <<END;
Usage: $0 [options] -- [WHICH FEATURES]
output GFF3 for selected database features
Options:
-d --dsn The database name ($DSN)
-a --adaptor The storage adaptor to use ($ADAPTOR)
-u --user User to connect to database as
-p --password Password to use to connect to database
-g --gff3opt flag options to gff3_string (i.e.: pass -gffopt 1 to recurse)
WHICH FEATURES: any remaining options after '--' will select
a subset of features. The arguments are identical to those
accepted by Bio::DB::SeqFeature::Store->features().
END
$ADAPTOR ||= 'DBI::mysql';
$DSN ||= $ADAPTOR eq 'DBI::mysql' ? "mysql_read_default_file=$ENV{HOME}/.my.cnf" : '';
my $store = Bio::DB::SeqFeature::Store->new(
-dsn => $DSN,
-adaptor => $ADAPTOR,
-user => $USER,
-pass => $PASS,
)
or die "Couldn't create connection to the database";
# on signals, give objects a chance to call their DESTROY methods
$SIG{TERM} = $SIG{INT} = sub { undef $store; die "Aborted..."; };
my $seq_stream = $store->get_seq_stream(@ARGV) or die "failed to get_seq_stream(@ARGV)";
while (my $seq = $seq_stream->next_seq) {
### 20100725 // genehack
# Try to call a gff3_string() method, but fall back to gff_string() if $seq
# doesn't support that. Note that gff_string() is required per
# Bio::SeqFeatureI, while gff3_string() is not. Currently, only
# Bio::SeqFeature::Lite implements gff3_string().
if ( $seq->can( 'gff3_string' )) {
print $seq->gff3_string(@gff3opt) . "\n";
}
elsif ( $seq->can( 'gff_string' )) {
# since we intend on getting a GFF3 string, make sure to pass the version
$seq->gff_format->gff_version(3);
print $seq->gff_string() . "\n";
}
else {
confess "sequence object $seq does not support gff3_string() or gff_string() methods!"
}
}
exit 0;
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