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CJFIELDS / BioPerl-1.7.8 / bin / bp_process_sgd 

            

              
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#!/usr/bin/perl
# This script will convert from SGD format to GFF format
# See http://db.yeastgenome.org/schema/Schema.html
use strict;
use warnings;
# hard-coded length data that I couldn't get directly
my %CHROMOSOMES = (I => 230_203,
                   II => 813_139,
                   III => 316_613,
                   IV  => 1_531_929,
                   V   => 576_869,
                   VI => 270_148,
                   VII => 1_090_937,
                   VIII => 562_639,
                   IX => 439_885,
                   X => 745_444,
                   XI => 666_445,
                   XII => 1_078_173,
                   XIII => 924_430,
                   XIV => 784_328,
                   XV  => 1_091_284,
                   XVI => 948_061,
                   Mit => 85_779);
my @ROMAN = qw(I II III IV V VI VII VIII IX X
               XI XII XIII XIV XV XVI Mit);
if ($ARGV[0] =~ /^--?h/) {
  die <<USAGE;
 Usage: $0 <SGD features file>
This script massages the SGD sequence annotation flat files located at
ftp://genome-ftp.stanford.edu/pub/yeast/data_dump/feature/chromosomal_features.tab
into a version of the GFF format suitable for display by the generic
genome browser.
To use this script, get the SGD chromosomal_features.tab file from the
FTP site listed above, and run the following command:
  % process_sgd.pl chromosomal_features.tab > yeast.gff
The yeast.gff file can then be loaded into a Bio::DB::GFF database
using the following command:
  % bulk_load_gff.pl -d <databasename> yeast.gff
USAGE
;
}
# first print out chromosomes
# We hard coded the lengths because they are not available in the features table.
for my $chrom (sort keys %CHROMOSOMES) {
  print join("\t",$chrom,'chromosome','Component',1,$CHROMOSOMES{$chrom},'.','.','.',qq(Sequence "$chrom")),"\n";
}
# this is hard because the SGD idea of a feature doesn't really map onto the GFF idea.
while (<>) {
  chomp;
  my($id,$gene,$aliases,$type,$chromosome,$start,$stop,$strand,$sgdid,$sgdid2,$description,$date) = split "\t";
  my $ref = $ROMAN[$chromosome-1];
  $description =~ s/"/\\"/g;
  $description =~ s/;/\\;/g;
  $strand = $strand eq 'W' ? '+' : '-';
  ($start,$stop) = ($stop,$start) if $strand eq '-';
  die "Strand logic is messed up" if $stop < $start;
  if ($gene) {
     my @aliases = split(/\|/,$aliases);
     my $aliases = join " ; ",map {qq(Alias "$_")} @aliases;
     my $group = qq(Gene "$gene" ; Note "$description");
     $group .= " ; $aliases" if $aliases;
     print join("\t",$ref,'sgd','gene',$start,$stop,'.',$strand,'.',$group),"\n";
     $description .= "\\; AKA @aliases" if @aliases;
  }
  print join("\t",$ref,'sgd',$type,$start,$stop,'.',$strand,'.',qq($type "$id" ; Note "$description")),"\n";
}
__END__
=head1 NAME
bp_process_sgd.pl - Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
=head1 SYNOPSIS
  % bp_process_sgd.pl chromosomal_features.tab > yeast.gff
=head1 DESCRIPTION
This script massages the SGD sequence annotation flat files located at
ftp://genome-ftp.stanford.edu/pub/yeast/data_dump/feature/chromosomal_features.tab
into a version of the GFF format suitable for display by the generic
genome browser.
To use this script, get the SGD chromosomal_features.tab file from the
FTP site listed above, and run the following command:
  % bp_process_sgd.pl chromosomal_features.tab > yeast.gff
The yeast.gff file can then be loaded into a Bio::DB::GFF database
using the following command:
  % bulk_load_gff.pl -d <databasename> yeast.gff
=head1 SEE ALSO
L<Bio::DB::GFF>, L<bulk_load_gff.pl>, L<load_gff.pl>
=head1 AUTHOR
Lincoln Stein, lstein@cshl.org
Copyright (c) 2002 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See DISCLAIMER.txt for
disclaimers of warranty.
=cut