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#!/usr/bin/perl -w
use strict;
use Getopt::Long;
use Bio::DB::Fasta;
my ($FASTA_DIR, $GFFFILENAME, $TYPE, $SOURCE, $ATTRIBUTES, $NOSEQUENCE);
GetOptions(
'fasta_dir=s' => \$FASTA_DIR,
'gfffilename=s' => \$GFFFILENAME,
'type=s' => \$TYPE,
'source=s' => \$SOURCE,
'attributes=s' => \$ATTRIBUTES,
'nosequence' => \$NOSEQUENCE,
) or ( system( 'pod2text', $0 ), exit -1 );
my $fastadir = $FASTA_DIR || './fasta';
my $gfffile = $GFFFILENAME || 'out.gff';
my $type = $TYPE || 'EST';
my $source = $SOURCE || '.';
-r $fastadir or die "fasta dir '$fastadir' not found or not readable\n";
open OUT, ">", $gfffile or die "couldn't open $gfffile for writing: $!\n";
my $stream = Bio::DB::Fasta->new($fastadir)->get_PrimarySeq_stream;
print OUT "##gff-version 3\n";
print OUT "#this file generated from $0\n";
while (my $seq = $stream->next_seq) {
my $atts;
if ($ATTRIBUTES) {
$atts = "ID=".$seq->id.";Name=".$seq->id.";$ATTRIBUTES";
}
else {
$atts = "ID=".$seq->id.";Name=".$seq->id;
}
print OUT join("\t",
$seq->id,
$source,
$type,
1,
$seq->length,
".",".",".",
$atts
),"\n";
}
if (!$NOSEQUENCE) {
print OUT "##FASTA\n";
#reset the seq stream
$stream = Bio::DB::Fasta->new($fastadir)->get_PrimarySeq_stream;
while (my $seq = $stream->next_seq) {
print OUT ">".$seq->id."\n";
print OUT $seq->seq . "\n";
}
}
close OUT;
=pod
=head1 NAME
$O - Convert FASTA to simple GFF3
=head1 SYNOPSYS
% $O [options]
=head1 COMMAND-LINE OPTIONS
--fasta_dir Directory contain fasta files
(default: ./fasta)
--gfffilename Name of GFF3 file to be created
(default: ./out.gff)
--type SO type to assign to each feature
(default: EST)
--source Text to appear in source column
(default: .)
--attributes Additional tag=value pairs to appear in column 9
--nosequence Suppress the ##FASTA section (ie, don't
print DNA sequences)
=head1 DESCRIPTION
This script simply takes a collection of fasta files and converts them
to simple GFF3 suitable for loading into chado.
=head1 AUTHORS
Scott Cain E<lt>cain@cshl.orgE<gt>
Copyright (c) 2006
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
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