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fixed process_gadfly script to accomodate release3 data; however this…
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… data is only genes so alignments are missing
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@lstein
lstein committed Jan 8, 2003
1 parent af83559 commit 3b8135d
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Showing 2 changed files with 116 additions and 44 deletions.
80 changes: 58 additions & 22 deletions bin/process_gadfly.PLS
View file
Expand Up @@ -19,23 +19,27 @@ $Config{startperl}
# In the following, perl variables are not expanded during extraction.

print OUT <<'!NO!SUBS!';
if ($ARGV[0]=~/^-?-h/i) {
if ($ARGV[0]=~/^-?-h/ || @ARGV < 1) {
die <<'USAGE';
This script massages the RELEASE 3 Flybase/Gadfly GFF file located at
http://www.fruitfly.org/sequence/sequence_db/whole-genome_annotation-feature-region_dmel_RELEASE3.GFF
into the "correct" version of the GFF format.
This script massages the RELEASE 3 Flybase/Gadfly GFF files located at
http://www.fruitfly.org/sequence/sequence_db into the "correct"
version of the GFF format.
To use this script, download the Gadfly GFF file and save it to disk.
Then run this script on the file:
To use this script, download the whole genome FASTA file and save it
to disk. (The downloaded file will be called something like
"na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the
HTML page doesn't give the filename.) Do the same for the whole
genome GFF annotation file (the saved file will be called something
like "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".) If
you wish you can download the ZIP compressed versions of these files.
% process_gadfly.pl whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
Next run this script on the two files, indicating the name of the
downloaded FASTA file first, followed by the gff file:
To load the fly DNA, download the FASTA format file for the
corresponding release in chromosome arm format
(e.g. http://www.fruitfly.org/sequence/sequence_db/na_whole-genome_genomic_dmel_RELEASE3.FASTA).
% process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
The gadfly.gff file and the fasta fiile can now be loaded into a Bio::DB::GFF database
The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database
using the following command:
% bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff
Expand Down Expand Up @@ -71,6 +75,16 @@ USAGE
use strict;
foreach (@ARGV) {
$_ = "gunzip -c $_ |" if /\.gz$/;
}
if ($ARGV[0] =~ /fasta/i) {
process_fasta();
} else {
die "call as process_gadfly.pl \"release3_dna.FASTA\" \"release3_features.GFF\"";
}
while (<>) {
next if /^\#/;
chomp;
Expand Down Expand Up @@ -105,6 +119,25 @@ sub dump_symbol {
print join("\t",$ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,qq(Symbol "$symbol")),"\n";
}
sub process_fasta {
my $file = shift @ARGV;
open F,$file or die "Can't open $file: $!";
print STDERR "Reading big FASTA file, please be patient...\n";
my ($current_id,%lengths);
while (<F>) {
if (/^>(\S+)/) {
$current_id = $1;
next;
}
die "this doesn't look like a fasta file to me" unless $current_id;
chomp;
$lengths{$current_id} += length;
}
foreach (sort keys %lengths) {
print join("\t",$_,'arm','Component',1,$lengths{$_},'.','+','.',qq(Sequence "$_")),"\n";
}
}
__END__
=head1 NAME
Expand All @@ -117,20 +150,24 @@ process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for
=head1 DESCRIPTION
This script massages the RELEASE 3 Flybase/Gadfly GFF file located at
http://www.fruitfly.org/sequence/sequence_db/whole-genome_annotation-feature-region_dmel_RELEASE3.GFF
into the "correct" version of the GFF format.
This script massages the RELEASE 3 Flybase/Gadfly GFF files located at
http://www.fruitfly.org/sequence/sequence_db into the "correct"
version of the GFF format.
To use this script, download the Gadfly GFF file and save it to disk.
Then run this script on the file:
To use this script, download the whole genome FASTA file and save it
to disk. (The downloaded file will be called something like
"na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the
HTML page doesn't give the filename.) Do the same for the whole
genome GFF annotation file (the saved file will be called something
like "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".) If
you wish you can download the ZIP compressed versions of these files.
% process_gadfly.pl whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
Next run this script on the two files, indicating the name of the
downloaded FASTA file first, followed by the gff file:
To load the fly DNA, download the FASTA format file for the
corresponding release in chromosome arm format
(e.g. http://www.fruitfly.org/sequence/sequence_db/na_whole-genome_genomic_dmel_RELEASE3.FASTA).
% process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
The gadfly.gff file and the fasta fiile can now be loaded into a Bio::DB::GFF database
The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database
using the following command:
% bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff
Expand Down Expand Up @@ -175,7 +212,6 @@ it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
=cut
!NO!SUBS!
close OUT or die "Can't close $file: $!";
chmod 0755, $file or die "Can't reset permissions for $file: $!\n";
Expand Down
80 changes: 58 additions & 22 deletions bin/process_gadfly.pl
View file
@@ -1,23 +1,26 @@
#!/usr/bin/perl


if ($ARGV[0]=~/^-?-h/i) {
if ($ARGV[0]=~/^-?-h/ || @ARGV < 1) {
die <<'USAGE';
This script massages the RELEASE 3 Flybase/Gadfly GFF file located at
http://www.fruitfly.org/sequence/sequence_db/whole-genome_annotation-feature-region_dmel_RELEASE3.GFF
into the "correct" version of the GFF format.
This script massages the RELEASE 3 Flybase/Gadfly GFF files located at
http://www.fruitfly.org/sequence/sequence_db into the "correct"
version of the GFF format.
To use this script, download the Gadfly GFF file and save it to disk.
Then run this script on the file:
To use this script, download the whole genome FASTA file and save it
to disk. (The downloaded file will be called something like
"na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the
HTML page doesn't give the filename.) Do the same for the whole
genome GFF annotation file (the saved file will be called something
like "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".) If
you wish you can download the ZIP compressed versions of these files.
% process_gadfly.pl whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
Next run this script on the two files, indicating the name of the
downloaded FASTA file first, followed by the gff file:
To load the fly DNA, download the FASTA format file for the
corresponding release in chromosome arm format
(e.g. http://www.fruitfly.org/sequence/sequence_db/na_whole-genome_genomic_dmel_RELEASE3.FASTA).
% process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
The gadfly.gff file and the fasta fiile can now be loaded into a Bio::DB::GFF database
The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database
using the following command:
% bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff
Expand Down Expand Up @@ -53,6 +56,16 @@

use strict;

foreach (@ARGV) {
$_ = "gunzip -c $_ |" if /\.gz$/;
}

if ($ARGV[0] =~ /fasta/i) {
process_fasta();
} else {
die "call as process_gadfly.pl \"release3_dna.FASTA\" \"release3_features.GFF\"";
}

while (<>) {
next if /^\#/;
chomp;
Expand Down Expand Up @@ -87,6 +100,25 @@ sub dump_symbol {
print join("\t",$ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,qq(Symbol "$symbol")),"\n";
}

sub process_fasta {
my $file = shift @ARGV;
open F,$file or die "Can't open $file: $!";
print STDERR "Reading big FASTA file, please be patient...\n";
my ($current_id,%lengths);
while (<F>) {
if (/^>(\S+)/) {
$current_id = $1;
next;
}
die "this doesn't look like a fasta file to me" unless $current_id;
chomp;
$lengths{$current_id} += length;
}
foreach (sort keys %lengths) {
print join("\t",$_,'arm','Component',1,$lengths{$_},'.','+','.',qq(Sequence "$_")),"\n";
}
}

__END__
=head1 NAME
Expand All @@ -99,20 +131,24 @@ =head1 SYNOPSIS
=head1 DESCRIPTION
This script massages the RELEASE 3 Flybase/Gadfly GFF file located at
http://www.fruitfly.org/sequence/sequence_db/whole-genome_annotation-feature-region_dmel_RELEASE3.GFF
into the "correct" version of the GFF format.
This script massages the RELEASE 3 Flybase/Gadfly GFF files located at
http://www.fruitfly.org/sequence/sequence_db into the "correct"
version of the GFF format.
To use this script, download the Gadfly GFF file and save it to disk.
Then run this script on the file:
To use this script, download the whole genome FASTA file and save it
to disk. (The downloaded file will be called something like
"na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the
HTML page doesn't give the filename.) Do the same for the whole
genome GFF annotation file (the saved file will be called something
like "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".) If
you wish you can download the ZIP compressed versions of these files.
% process_gadfly.pl whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
Next run this script on the two files, indicating the name of the
downloaded FASTA file first, followed by the gff file:
To load the fly DNA, download the FASTA format file for the
corresponding release in chromosome arm format
(e.g. http://www.fruitfly.org/sequence/sequence_db/na_whole-genome_genomic_dmel_RELEASE3.FASTA).
% process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
The gadfly.gff file and the fasta fiile can now be loaded into a Bio::DB::GFF database
The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database
using the following command:
% bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff
Expand Down

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