Perl script - "$orthomclparser" requires explicit package name

[roro]

Hello,

Whenever I try to run this script, I get the following error on command line: "Can't call method "parse" on an undefined value at....". Also, my debugger keeps telling me that "$orthomclparser requires explicit package name". Any help would be appreciated as I am very new to Perl.


#!/usr/bin/perl

use OBO::Core::RelationshipType;
use OBO::Core::Relationship;
use OBO::Core::Term;
use OBO::CCO::CCO_ID_Term_Map;
use OBO::Core::Ontology;

use strict;
use warnings;
use Carp;

$OrthoMCLParser->parse();
$OrthoMCLParser-> work();


sub new {
my $class = $_[0];
my $self = {};

bless( $self, $class );
return $self;
}

sub parse {
my $self = shift;
# get orthoMCL data file
my $omclDataFile = shift;
open(my $FH, '<', $omclDataFile) || die "Cannot open file '$omclDataFile': $!";

# parse orthoMCL output
my %clusters; # %clusters{protein_name}{taxon_label}
while(<$FH>){
my ($cluster, $proteins) = split /:\s+/xms;
my $cluster_num = $.-1;
$cluster = $cluster_num;
my @proteins = split /\s/xms, $proteins;
foreach ( @proteins) {
$_ =~/\A(\w+?)\((\w+?)\)/xms; # $1 is protein name, $2 is taxon label (e.g Hsa)
$clusters{$cluster}->{$1} = $2;
}
}
close $FH;
return \%clusters;
}

sub work {
my ($self, $clust, $files, $tax) = @_;
my %clusters = %{$clust};
my %taxa = %{$tax};
# input/output files
my ($new_OBO_file, $u_map_file, $t_map_file, $o_map_file, $b_map_file) = @{$files};

# Initialize maps (OBO::CCO::CCO_ID_Term_Map objects)
my $u_map = OBO::CCO::CCO_ID_Term_Map->new($u_map_file); # map for Upper Level Ontology terms
my $t_map = OBO::CCO::CCO_ID_Term_Map->new($t_map_file); # map for taxonomy terms
my $o_map = OBO::CCO::CCO_ID_Term_Map->new($o_map_file); # map for orthologous groups terms
my $b_map = OBO::CCO::CCO_ID_Term_Map->new($b_map_file); # map for biomolecule terms
# taxon specific maps for biolmolecule terms
foreach (keys %taxa) {
push @{$taxa{$_}}, OBO::CCO::CCO_ID_Term_Map->new($taxa{$_}->[1]);
}
# @{$taxa{taxon_label}} contains now taxon name, taxon specific map file, taxon specific map object

my $ontology = OBO::Core::Ontology->new();

# populate ontology
$ontology->add_relationship_type_as_string ('is_a', 'is_a');
$ontology->add_relationship_type_as_string ('has_source', 'has_source');
#$ontology->add_relationship_type_as_string ('source_of', 'source_of');

my $protein = OBO::Core::Term->new();# upper level ontology term
$protein->name('protein');
$protein->id(assign_term_id($u_map, 'U', 'protein'));
if ($u_map->contains_value('protein')) {
$protein->id($u_map->get_cco_id_by_term('protein'));
}else{
$protein->id(assign_term_id($u_map, 'U', 'protein'));
}
$ontology->add_term($protein);

foreach (keys %taxa) {
my $taxon = OBO::Core::Term->new();
my $taxon_lab = $_;
my $tax_name = $taxa{$taxon_lab}->[0];
$taxon->name($tax_name);
$taxon->id(assign_term_id($t_map, 'T', $tax_name));
$ontology->add_term($taxon);
push @{$taxa{$taxon_lab}}, $taxon;
#@{$taxa{$taxon_lab}} contains now taxon name, taxon specific map file, taxon specific map object, taxon term object
}

foreach (keys %clusters) {
my $cluster = OBO::Core::Term->new();
my $clust_num = $_;
my $clust_name = "Type $_ protein";
$cluster->name($clust_name);
$cluster->id(assign_term_id($o_map, 'O', $clust_name));
$cluster->def_as_string("A protein belonging to the orthological type $_ produced by orthoMCL", "[CCO:vm]");
$ontology->create_rel($cluster, 'is_a', $protein);
foreach (keys %{$clusters{$clust_num}}) { # for each protein in the cluster
my $prot_name = $_;
my $taxon_lab = $clusters{$clust_num}{$prot_name};
my $clust_protein = OBO::Core::Term->new();
$clust_protein->name($prot_name);
$clust_protein->id(assign_biomol_id($taxa{$taxon_lab}[2], $b_map, $prot_name));
my $short_map = $taxa{$taxon_lab}[2];
if ($short_map->contains_value($prot_name)) {
$clust_protein->id($short_map->get_cco_id_by_term($prot_name));
} else {
$clust_protein->id(assign_biomol_id($short_map, $b_map, $prot_name));
}
$ontology->add_term($clust_protein);
$ontology->create_rel($clust_protein, 'is_a', $cluster);

$ontology->create_rel($clust_protein, 'has_source', $taxa{$taxon_lab}->[3]);
#$ontology->create_rel($taxa{$taxon_lab}->[3], 'source_of', $clust_protein);
}
}

# Write the new ontology and maps to disk
open (my $FH, ">".$new_OBO_file) || die "Cannot write OBO file: ", $!;
$ontology->export(\*$FH);
close $FH;
foreach ((keys %taxa)) {
$taxa{$_}[2] -> write_map();
}
$b_map -> write_map();
$o_map -> write_map();
$t_map -> write_map();
$u_map -> write_map();
return $ontology;
}

[oesxyl]

Hello,

Whenever I try to run this script, I get the following error on command line: "Can't call method "parse" on an undefined value at....". Also, my debugger keeps telling me that "$orthomclparser requires explicit package name". Any help would be appreciated as I am very new to Perl.


#!/usr/bin/perl

use OBO::Core::RelationshipType;
use OBO::Core::Relationship;
use OBO::Core::Term;
use OBO::CCO::CCO_ID_Term_Map;
use OBO::Core::Ontology;

use strict;
use warnings;
use Carp;

$OrthoMCLParser->parse();
$OrthoMCLParser-> work();


sub new {
my $class = $_[0];
my $self = {};

bless( $self, $class );
return $self;
}

sub parse {
my $self = shift;
# get orthoMCL data file
my $omclDataFile = shift;
open(my $FH, '<', $omclDataFile) || die "Cannot open file '$omclDataFile': $!";

# parse orthoMCL output
my %clusters; # %clusters{protein_name}{taxon_label}
while(<$FH>){
my ($cluster, $proteins) = split /:\s+/xms;
my $cluster_num = $.-1;
$cluster = $cluster_num;
my @proteins = split /\s/xms, $proteins;
foreach ( @proteins) {
$_ =~/\A(\w+?)\((\w+?)\)/xms; # $1 is protein name, $2 is taxon label (e.g Hsa)
$clusters{$cluster}->{$1} = $2;
}
}
close $FH;
return \%clusters;
}

sub work {
my ($self, $clust, $files, $tax) = @_;
my %clusters = %{$clust};
my %taxa = %{$tax};
# input/output files
my ($new_OBO_file, $u_map_file, $t_map_file, $o_map_file, $b_map_file) = @{$files};

# Initialize maps (OBO::CCO::CCO_ID_Term_Map objects)
my $u_map = OBO::CCO::CCO_ID_Term_Map->new($u_map_file); # map for Upper Level Ontology terms
my $t_map = OBO::CCO::CCO_ID_Term_Map->new($t_map_file); # map for taxonomy terms
my $o_map = OBO::CCO::CCO_ID_Term_Map->new($o_map_file); # map for orthologous groups terms
my $b_map = OBO::CCO::CCO_ID_Term_Map->new($b_map_file); # map for biomolecule terms
# taxon specific maps for biolmolecule terms
foreach (keys %taxa) {
push @{$taxa{$_}}, OBO::CCO::CCO_ID_Term_Map->new($taxa{$_}->[1]);
}
# @{$taxa{taxon_label}} contains now taxon name, taxon specific map file, taxon specific map object

my $ontology = OBO::Core::Ontology->new();

# populate ontology
$ontology->add_relationship_type_as_string ('is_a', 'is_a');
$ontology->add_relationship_type_as_string ('has_source', 'has_source');
#$ontology->add_relationship_type_as_string ('source_of', 'source_of');

my $protein = OBO::Core::Term->new();# upper level ontology term
$protein->name('protein');
$protein->id(assign_term_id($u_map, 'U', 'protein'));
if ($u_map->contains_value('protein')) {
$protein->id($u_map->get_cco_id_by_term('protein'));
}else{
$protein->id(assign_term_id($u_map, 'U', 'protein'));
}
$ontology->add_term($protein);

foreach (keys %taxa) {
my $taxon = OBO::Core::Term->new();
my $taxon_lab = $_;
my $tax_name = $taxa{$taxon_lab}->[0];
$taxon->name($tax_name);
$taxon->id(assign_term_id($t_map, 'T', $tax_name));
$ontology->add_term($taxon);
push @{$taxa{$taxon_lab}}, $taxon;
#@{$taxa{$taxon_lab}} contains now taxon name, taxon specific map file, taxon specific map object, taxon term object
}

foreach (keys %clusters) {
my $cluster = OBO::Core::Term->new();
my $clust_num = $_;
my $clust_name = "Type $_ protein";
$cluster->name($clust_name);
$cluster->id(assign_term_id($o_map, 'O', $clust_name));
$cluster->def_as_string("A protein belonging to the orthological type $_ produced by orthoMCL", "[CCO:vm]");
$ontology->create_rel($cluster, 'is_a', $protein);
foreach (keys %{$clusters{$clust_num}}) { # for each protein in the cluster
my $prot_name = $_;
my $taxon_lab = $clusters{$clust_num}{$prot_name};
my $clust_protein = OBO::Core::Term->new();
$clust_protein->name($prot_name);
$clust_protein->id(assign_biomol_id($taxa{$taxon_lab}[2], $b_map, $prot_name));
my $short_map = $taxa{$taxon_lab}[2];
if ($short_map->contains_value($prot_name)) {
$clust_protein->id($short_map->get_cco_id_by_term($prot_name));
} else {
$clust_protein->id(assign_biomol_id($short_map, $b_map, $prot_name));
}
$ontology->add_term($clust_protein);
$ontology->create_rel($clust_protein, 'is_a', $cluster);

$ontology->create_rel($clust_protein, 'has_source', $taxa{$taxon_lab}->[3]);
#$ontology->create_rel($taxa{$taxon_lab}->[3], 'source_of', $clust_protein);
}
}

# Write the new ontology and maps to disk
open (my $FH, ">".$new_OBO_file) || die "Cannot write OBO file: ", $!;
$ontology->export(\*$FH);
close $FH;
foreach ((keys %taxa)) {
$taxa{$_}[2] -> write_map();
}
$b_map -> write_map();
$o_map -> write_map();
$t_map -> write_map();
$u_map -> write_map();
return $ontology;
}


please put your code between [ code] and [ /code] tags. You can edit your previous post to do that.
Did you have onto-perl installed?

also, do you call this from another script? I don't see where $OrthoMCLParser is created
best regards

[roro]

Hi,

Yes I have onto-perl installed. And I believe the OrthoMCLParser is a perl module that comes with onto-perl.

[oesxyl]

Hi,

Yes I have onto-perl installed. And I believe the OrthoMCLParser is a perl module that comes with onto-perl.
onto-perl come with two parsers, for OBO and OWL ontologies and for both you must first create the parser with new and then pass an argument to work method, the ontology you want to parse.

this script look more like a package, :)
best regards

[roro]

Thanks for the quick reply. Could you provide me examples of what you mean? I am sorry, but I am quite new to this (it has already been a steep learning curve). How could I fix it?

Thanks so much.

[oesxyl]

Thanks for the quick reply. Could you provide me examples of what you mean? I am sorry, but I am quite new to this (it has already been a steep learning curve). How could I fix it?

Thanks so much.
your script looks like this one:

http://cpansearch.perl.org/src/EASR/ONTO-PERL-1.13/OBO/CCO/OrthoMCLParser.pm

which is a module in onto-perl 1.13. Is my fault that I don't know about it, :)

http://search.cpan.org/~easr/ONTO-PERL-1.13/

you have examples of scripts to the "Other files" section.

best regards