Sac cer annotations
===================

cytoband.txt = http://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/database/chromInfo.txt.gz             06-Oct-2011 
and processed it with the script below:
perl -aF/\\t/ -ne 'chomp; /^chr/ or next; print join("\t",$F[0],0,$F[1],"","gneg"),"\n"' < chromInfo.txt | sort > cytoband.txt

annotations.txt and genes.txt are obtained by running the script below

#Go to http://www.ensembl.org/biomart/martview/ and select organism and build and select the following attribs.
# Ensembl Gene ID, Ensembl Transcript ID , Chromosome Name,   Gene Start (bp) , Gene End (bp),Strand,Transcript Start (bp), Transcript End (bp),
tail --line=+2 genes_mart_export.txt | perl -aF/\\t/ -ne 'chomp($F[7]);print join("\t",@F[0,1],"chr".$F[2],$F[5] =~ /^-/ ? "-" : "+",@F[3,4,6,7],1,$F[6].",",$F[7].","),"\n"' > genes.txt
# Ensembl Gene ID,  Associated Gene name, Description, GO Term Name, Gene Ontology Name - bp, cc ,mf or GO Domain (biol proc..), Entrez gene Id 
perl ~/convertBioMartGO2annotations.pl annot_mart_export.txt > annotations.txt

The perl script - convertBioMartGO2annotations.pl 

#!/bin/perl
# usage: perl ~/convertBioMartGO2annotations.pl annot_mart_export.txt > annotations.txt
use strict;
my %annos;
while (<>)
{
	chomp; s/\cM|\cJ//g;
	my ($id, $name,$desc,$go, $domain ,$locus) = split /\t/;
	$annos{$id}{id} = [$desc, $name, $locus];
	$annos{$id}{$domain}{$go}++;
}
print "Symbol\tName\tDescription\tBiological process\tCellular component\tMolecular function\tLocusLink ID\tOther Aliases\n";
for my $id (sort keys %annos)
{
	my ($desc, $name, $locus) = @{$annos{$id}{id}};
	print join("\t",$id,$name,$desc,map {join(", ",sort keys %{$annos{$id}{$_}})} qw(biological_process cellular_component molecular_function),$locus,$name),"\n";
}
