#!/usr/bin/perl
if ($ARGV[0]=~/^-?-h/ || @ARGV < 1) {
die <<'USAGE';
This script massages the RELEASE 3 Flybase/Gadfly GFF files located at
"correct" version of the GFF format.
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.
Next run this script on the two files, indicating the name of the
downloaded FASTA file first, followed by the gff file:
% 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 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
(Where "fly" is the name of the database. Change it as appropriate.
The database must already exist and be writable by you!)
The resulting database will have the following feature types
(represented as "method:source"):
Component:arm A chromosome arm
Component:scaffold A chromosome scaffold (accession #)
Component:gap A gap in the assembly
clone:clonelocator A BAC clone
gene:gadfly A gene accession number
transcript:gadfly A transcript accession number
translation:gadfly A translation
codon:gadfly Significance unknown
exon:gadfly An exon
symbol:gadfly A classical gene symbol
similarity:blastn A BLASTN hit
similarity:blastx A BLASTX hit
similarity:sim4 EST->genome using SIM4
similarity:groupest EST->genome using GROUPEST
similarity:repeatmasker A repeat
IMPORTANT NOTE: This script will *only* work with the RELEASE3 gadfly
files and will not work with earlier releases.
USAGE
;
}
foreach (@ARGV) {
$_ = "gunzip -c $_ |" if /\.gz$/;
}
if ($ARGV[0] =~ /fasta/i) {
process_fasta();
} else {
die "call as process_gadfly.pl \"release3_dna.FASTA\" \"release3_features.GFF\"";
}
while (<>) {
next if /^\
chomp;
my ($ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,$cgroup) = split "\t";
next if $start > $stop;
my $fixed_group = fix_group($csource,$cmethod,$cgroup);
print join("\t",$ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,$fixed_group),"\n";
dump_symbol($ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,$cgroup) if $cgroup =~ /symbol/i;
}
sub fix_group {
my ($source,$method,$group) = @_;
my (@group,$gene);
push @group,"Transcript $1" if $group =~ /transgrp=([^; ]+)/;
push @group,"Gene $1" if $method eq 'gene' && $group =~ /genegrp=([^; ]+)/;
$gene ||= qq(Note "FlyBase $1") if $group =~ /dbxref=FlyBase:(\w+)/;
$gene ||= qq(Note "GadFly $1") if $group =~ /genegrp=([^; ]+)/;
push @group,qq(Note "Symbol $1") if $group =~ /symbol=([^; ]+)/ && "Gene $1" ne $group[0];
push @group,$gene;
return join ' ; ',@group;
}
sub dump_symbol {
my ($ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,$cgroup) = @_;
my ($symbol) = $cgroup=~/symbol=([^;]+)/;
my ($gene) = $cgroup=~/genegrp=([^;]+)/;
return if $symbol eq $gene;
$cmethod = 'symbol';
print join("\t",$ref,$csource,$cmethod,$start,$stop,$cscore,$strand,$cphase,qq(Symbol "$symbol")),"\n";
}
sub process_fasta {
my $file = shift @ARGV;
open my $F, '<', $file or die "Could not read file '$file': $!\n";
print STDERR "Reading big FASTA file, please be patient...\n";
my ($current_id,%lengths);
while (my $line = <$F>) {
if ($line =~ /^>(\S+)/) {
$current_id = $1;
next;
}
die "this doesn't look like a fasta file to me" unless $current_id;
chomp $line;
$lengths{$current_id} += length $line;
}
close $F;
foreach my $id (sort keys %lengths) {
print join("\t", $id, 'arm', 'Component', 1, $lengths{$id},
'.', '+', '.', qq(Sequence "$id")
), "\n";
}
}