Hi,
I'm using this module: http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Ontology/GOterm.html
for a project and I'm supposed to create a new GOTerm object and pass in a GO_Id. I'm trying to print out the description of the GOTerm with to_String but every single description is empty. Under "obsolete" a 0 is printed. How do I fix this? The GOTerms are in the right format.
Thank you.
#!/usr/bin/perl -w
use Bio::Ontology::GOterm;
use strict;
# Read in ccds file for parsing
my $in = "";
# Use subroutines parse file and send gene
# names to Bio::GO module to get the go_id,
# definition
GeneList('1');# For chromosome 1. If this was a method, $in would be passed in. I'm passing in a specification for chromosome 1.
############### Subs #########################
sub GeneList{ # Pass in the chromosomes you want to check.
my @chromosomes = @_;
my %genelist; # This gives a nonredundant gene list. The keys are the gene IDs or names and the
# values are references to the arrays of other information.
# Only the last gene entry for a certain gene will be stored. Length of that sequence
# may differ from the other gene entries though.
open(IN, $in)|| die "Error: $!\n";
my $out = ">";
open(OUT, $out);
my @IN2 = split(/\r/,<IN>); # <IN> sends back a giant string because lines are delimited by \r instead of \n
foreach(@IN2){
my @fields = split(/\t/);
# Skip "withdrawn" in ccds_status field, check if the first line is skipped
if($fields[5] ne 'Public') {next};
if (!grep(/^$fields[0]$/, @chromosomes)) {next};
# Remove redundancy in the list. If gene name exist more than once,
# then we are to remove the extra names.
$genelist{$fields[3]} = \@fields; # The above lines already avoid the withdrawn sequences and
# sequences not on chromosome 1.
}
foreach my $gene(keys %genelist){ # after redundancy is removed
foreach my $arr(@{GOTerms($gene, $genelist{$gene})}){ # print out each item in the returned list
if($arr){
print OUT $arr;
}
}
print OUT "\n"; # then make sure there is a nextline
}
close(OUT);
my $ref = \%genelist;
return $ref;
}
sub GOTerms{ # This will take one ID at a time, along with an array reference.
my $ID = $_[0];
my @array = @{$_[1]};
if(length($ID) > 7){$ID = '0000000';} # GO numbers maximum 7 digits
my $zeros = '0'x(7 - length($ID)); # to make the ID 7 characters long
# create a go terms object
my $go_term = Bio::Ontology::GOterm->new(-go_id => "GO:$zeros$ID");# Can -go_id => "GO:$ID" work? Or does it need all arguments?
# implement the methods Go_id and to_string of this object to
# return a list that is formatted like so:
# chr#\tgene_name\tGO_id\tGOTerm
# chr1 stat1 GO:0003947 The term description
#$go_term->GO_id("GO:$zeros$ID");# This should take in "GO_REF:$zeros$ID"
print $go_term->GO_id()."\n";
my @gene = ("chr$array[0]", "\t", $array[2], "\t", $go_term->GO_id(), "\t", $go_term->to_string());
return \@gene;
}
