Perl Error - Global symbol requires explicit package name - perl

Question

I am getting some errors while trying to run a Perl file which is I need to run. (I usually use Python but I do not know any other programming languages including Perl.) I will show errors firstly, then I will attach the whole code in the end.
The error:
$ perl C:/databases/ModelSEEDDatabase/Scripts/Archived_Perl_Scripts/DumpSOLRTables_Master.pl
Global symbol "$fba" requires explicit package name (did you forget to declare "my $fba"?) at C:/databases/ModelSEEDDatabase/Scripts/Archived_Perl_Scripts/DumpSOLRTables_Master.pl line 171.
Global symbol "$fba" requires explicit package name (did you forget to declare "my $fba"?) at C:/databases/ModelSEEDDatabase/Scripts/Archived_Perl_Scripts/DumpSOLRTables_Master.pl line 172.
Global symbol "$fba" requires explicit package name (did you forget to declare "my $fba"?) at C:/databases/ModelSEEDDatabase/Scripts/Archived_Perl_Scripts/DumpSOLRTables_Master.pl line 173.
Global symbol "$fba" requires explicit package name (did you forget to declare "my $fba"?) at C:/databases/ModelSEEDDatabase/Scripts/Archived_Perl_Scripts/DumpSOLRTables_Master.pl line 174.
Global symbol "$map" requires explicit package name (did you forget to declare "my $map"?) at C:/databases/ModelSEEDDatabase/Scripts/Archived_Perl_Scripts/DumpSOLRTables_Master.pl line 202.
Global symbol "$pmap" requires explicit package name (did you forget to declare "my $pmap"?) at C:/databases/ModelSEEDDatabase/Scripts/Archived_Perl_Scripts/DumpSOLRTables_Master.pl line 233.
Execution of C:/databases/ModelSEEDDatabase/Scripts/Archived_Perl_Scripts/DumpSOLRTables_Master.pl aborted due to compilation errors.
When I put "my" at before global symbols which are mentioned in the error, this time I am getting another error below:
$ perl C:/databases/ModelSEEDDatabase/Scripts/Archived_Perl_Scripts/DumpSOLRTables_Master.pl
"my" variable $fba masks earlier declaration in same statement at C:/databases/ModelSEEDDatabase/Scripts/Archived_Perl_Scripts/DumpSOLRTables_Master.pl line 172.
"my" variable $fba masks earlier declaration in same statement at C:/databases/ModelSEEDDatabase/Scripts/Archived_Perl_Scripts/DumpSOLRTables_Master.pl line 173.
"my" variable $fba masks earlier declaration in same statement at C:/databases/ModelSEEDDatabase/Scripts/Archived_Perl_Scripts/DumpSOLRTables_Master.pl line 174.
So, I do not know what should I do now actually. This Perl script will dump/extract two necessary files which are "ComplexRoles.tsv" and "TemplateReactions.tsv".
I am using Python 3.7 and Cygwin64. ModelSEEDDatabase Github link:
https://github.com/ModelSEED/ModelSEEDDatabase
If you can help me, I would be really glad. Thank you in advance.
The whole script is below: (I indicated the problematic lines which are 171, 172, 173, 174, 202, 233.)
#!/usr/bin/env perl
use warnings;
use strict;
use Getopt::Long::Descriptive;
my ($opt, $usage) = describe_options("%c %o <directory>",
[ "compounds=s", "path to master compounds file", { default => "../Biochemistry/compounds.master.tsv" } ],
[ "compartments=s", "path to master compartments file", { default => "../Biochemistry/compartments.master.tsv" } ],
[ "reactions=s", "path to master reactions file", { default => "../Biochemistry/reactions.master.tsv" } ],
[ "aliasdir=s", "path to directory with alias files", { default => "../Aliases/" } ],
[ "pathwaydir=s", "path to directory with pathway files", { default => "../Pathways/" } ],
[ "structuredir=s", "path to directory with structure files", { default => "../Structures/" } ],
[ "master=s", "path to output master biochemistry json file", { default => "../Biochemistry/biochemistry.master.json" } ],
[ "help|h", "print usage message and exit" ]
);
print($usage->text), exit if $opt->help;
my $directory = $ARGV[0];
exit if !$directory || !-d $directory;
$directory.="/" if $directory !~ /\/$/;
my #temp=();
my $header = 1;
#######################################################
#Initialization
#######################################################
#Collect Aliases
opendir(my $AliasDir, $opt->aliasdir);
my #Files = grep { $_ =~ /\.aliases$/ } readdir($AliasDir);
closedir($AliasDir);
my $rxn_alias_hash = {};
my $p_rxn_alias_hash = {};
my $cpd_alias_hash = {};
my $p_cpd_alias_hash = {};
my %alias_cpd_hash = ();
my %alias_rxn_hash = ();
foreach my $file (sort #Files){
$file =~ /^(\w+)\.aliases/;
my $aliasSet = $1;
$aliasSet = join(" ", split(/_/,$aliasSet)) if $aliasSet eq "Enzyme_Class";
open(FH, "< ".$opt->aliasdir.$file);
$header = 1;
while(<FH>){
chomp;
if($header){$header--;next}
#temp=split(/\t/,$_,-1);
if($temp[1] =~ /^cpd/ || $temp[2] =~ /^cpd/){
foreach my $cpd (split(/\|/,$temp[1])){
$cpd_alias_hash->{$aliasSet}->{$temp[0]}->{$cpd}=1;
$alias_cpd_hash{$cpd}{$aliasSet}{$temp[0]}=1;
}
foreach my $cpd (split(/\|/,$temp[2])){
$p_cpd_alias_hash->{$aliasSet}->{$temp[0]}->{$cpd}=1;
#Need to revise the decision to forgo aliases found in more recent database
if(!exists($alias_cpd_hash{$cpd}) && !exists($alias_cpd_hash{$cpd}{$aliasSet})){
$alias_cpd_hash{$cpd}{$aliasSet}{$temp[0]}=1;
}
}
}
if($temp[1] =~ /^rxn/ || $temp[2] =~ /^rxn/){
foreach my $rxn (split(/\|/,$temp[1])){
$rxn_alias_hash->{$aliasSet}->{$temp[0]}->{$rxn}=1;
$alias_rxn_hash{$rxn}{$aliasSet}{$temp[0]}=1;
}
foreach my $rxn (split(/\|/,$temp[2])){
$p_rxn_alias_hash->{$aliasSet}->{$temp[0]}->{$rxn}=1;
#Need to revise the decision to forgo aliases found in more recent database
if(!exists($alias_rxn_hash{$rxn}) && !exists($alias_rxn_hash{$rxn}{$aliasSet})){
$alias_rxn_hash{$rxn}{$aliasSet}{$temp[0]}=1;
}
}
}
}
close(FH);
}
my $rxn_pathways = {};
open(my $fh, "< ".$opt->pathwaydir."HopeScenarios.txt");
while (my $line = <$fh>) {
chomp($line);
my $array = [split(/\t/,$line)];
my $patharray = [split(/:/,$array->[0])];
pop(#{$patharray});
pop(#{$patharray});
if (defined($rxn_alias_hash->{KEGG}->{$array->[1]})) {
foreach my $rxn (keys(%{$rxn_alias_hash->{KEGG}->{$array->[1]}})) {
$rxn_pathways->{$rxn}->{KEGG}->{$patharray->[0]} = 1;
$rxn_pathways->{$rxn}->{Scenario}->{join("/",#{$patharray})} = 1;
}
} elsif (defined($p_rxn_alias_hash->{KEGG}->{$array->[1]})) {
foreach my $rxn (keys(%{$p_rxn_alias_hash->{KEGG}->{$array->[1]}})) {
$rxn_pathways->{$rxn}->{KEGG}->{$patharray->[0]} = 1;
$rxn_pathways->{$rxn}->{Scenario}->{join("/",#{$patharray})} = 1;
}
}
}
close($fh);
open($fh, "< ".$opt->pathwaydir."plantdefault.pathways.tsv");
my #headers = split(/\t/,<$fh>);
shift(#headers);
chomp($headers[$#headers]);
while(<$fh>){
chomp;
#temp=split(/\t/,$_,-1);
my $id = shift (#temp);
for(my $i=0;$i<scalar(#headers);$i++){
next if $temp[$i] eq "null";
foreach my $path (split(/\|/,$temp[$i])){
$rxn_pathways->{$id}{$headers[$i]}{$temp[$i]}=1;
}
}
}
close($fh);
my $cpd_structure = {};
open($fh, "< ".$opt->structuredir."KEGG_Charged_InChI.txt");
while (my $line = <$fh>) {
chomp($line);
my $array = [split(/\t/,$line)];
if (defined($cpd_alias_hash->{KEGG}->{$array->[0]})) {
foreach my $cpdid (keys(%{$cpd_alias_hash->{KEGG}->{$array->[0]}})){
if (!defined($cpd_structure->{$cpdid})) {
$cpd_structure->{$cpdid} = $array->[1];
}
}
}
if (defined($p_cpd_alias_hash->{KEGG}->{$array->[0]})) {
foreach my $cpdid (keys(%{$p_cpd_alias_hash->{KEGG}->{$array->[0]}})){
if (!defined($cpd_structure->{$cpdid})) {
$cpd_structure->{$cpdid} = $array->[1];
}
}
}
}
close($fh);
open($fh, "< ".$opt->structuredir."MetaCyc_Charged_InChI.txt");
while (my $line = <$fh>) {
chomp($line);
my $array = [split(/\t/,$line)];
if (defined($cpd_alias_hash->{MetaCyc}->{$array->[0]})) {
foreach my $cpdid (keys(%{$cpd_alias_hash->{MetaCyc}->{$array->[0]}})){
if (!defined($cpd_structure->{$cpdid})) {
$cpd_structure->{$cpdid} = $array->[1];
}
}
}
if (defined($p_cpd_alias_hash->{MetaCyc}->{$array->[0]})) {
foreach my $cpdid (keys(%{$p_cpd_alias_hash->{MetaCyc}->{$array->[0]}})){
if (!defined($cpd_structure->{$cpdid})) {
$cpd_structure->{$cpdid} = $array->[1];
}
}
}
}
close($fh);
#Retreiving templates
# Need to get these from source file
my $templates = [
$fba->_get_msobject("ModelTemplate","KBaseTemplateModels","GramPosModelTemplate"), ###line171
$fba->_get_msobject("ModelTemplate","KBaseTemplateModels","GramNegModelTemplate"), ###line172
$fba->_get_msobject("ModelTemplate","KBaseTemplateModels","CoreModelTemplate"), ###line173
$fba->_get_msobject("ModelTemplate","KBaseTemplateModels","PlantModelTemplate") ###line174
];
#Printing template table
my $templatlist = ["template.0","template.1","template.2","template.3"];
my $templatedata = [
["template.0","gram_positive_template","genome_scale_model","Bacteria","0","1","chenry"],
["template.1","gram_negative_template","genome_scale_model","Bacteria","0","1","chenry"],
["template.2","core_template","core_model","Bacteria","0","1","chenry"],
["template.3","plant_template","genome_scale_model","Plant","0","1","seaver"],
];
#Printing complex roles
open($fh, ">", $directory."ComplexRoles.tsv");
my $columns = [qw(
complex_id
complex_name
complex_source
complex_type
role_id
role_name
role_type
role_source
role_aliases
role_exemplar
type
triggering
optional
)];
print $fh join("\t",#{$columns})."\n";
my $cpxs = $map->complexes(); # Need to get these from source file ###line202
my $idhash;
my $count=0;
for (my $i=0; $i < #{$cpxs}; $i++) {
my $cpx = $cpxs->[$i];
$idhash->{$cpx->id()} = "cpx.".$i;
my $cpxroles = $cpx->complexroles();
for (my $j=0; $j < #{$cpxroles}; $j++) {
my $cpxrole = $cpxroles->[$j];
my $roleid = $cpxrole->role()->id();
$roleid =~ s/ms//;
my $data = [
"cpx.".$i,
"cpx.".$i,
"ModelSEED",
"SEED_role_complex",
$roleid,
$cpxrole->role()->name(),
"SEED_role",
"SEED",
"searchname:".$cpxrole->role()->searchname(),
"null",
"role_mapping",
$cpxrole->triggering(),
$cpxrole->optionalRole(),
];
print $fh join("\t",#{$data})."\n";
}
$count = $i;
}
$cpxs = $pmap->complexes(); # Need to get these from source file ###line233
for (my $i=0; $i < #{$cpxs}; $i++) {
$count++;
my $cpx = $cpxs->[$i];
$idhash->{$cpx->id()} = "cpx.".$count;
my $cpxroles = $cpx->complexroles();
for (my $j=0; $j < #{$cpxroles}; $j++) {
my $cpxrole = $cpxroles->[$j];
my $roleid = $cpxrole->role()->id();
$roleid =~ s/ms//;
my $data = [
"cpx.".$count,
"cpx.".$count,
"ModelSEED",
"SEED_role_complex",
$roleid,
$cpxrole->role()->name(),
"SEED_role",
"SEED",
"searchname:".$cpxrole->role()->searchname(),
"null",
"role_mapping",
$cpxrole->triggering(),
$cpxrole->optionalRole(),
];
print $fh join("\t",#{$data})."\n";
}
}
close($fh);
#Printing compounds
#As it stands, it's a copy of the master compounds file with the aliases integrated
open(FH, "< ".$opt->compounds);
open($fh, ">", $directory."Compounds.tsv");
$header = 1;
undef(#headers);
my %Compounds=();
while(<FH>){
chomp;
if($header){
#headers = split(/\t/,$_,-1);
print $fh $_."\n";
$header--;
next;
}
#temp=split(/\t/,$_,-1);
#map values to keys
#probably not that necessary, but useful if column order changes
my %cpdHash=();
for(my $i=0;$i<scalar(#headers);$i++){
$cpdHash{$headers[$i]}=$temp[$i];
}
my #aliases = ();
foreach my $aliasSet (keys %{$alias_cpd_hash{$cpdHash{id}}}){
foreach my $alias (keys %{$alias_cpd_hash{$cpdHash{id}}{$aliasSet}}){
push(#aliases, "\"".$aliasSet.":".$alias."\"");
}
}
$cpdHash{aliases}= scalar(#aliases)>0 ? join(";",#aliases) : "null";
print $fh join("\t", map { $cpdHash{$_} } #headers),"\n";
$Compounds{$cpdHash{id}}=\%cpdHash;
}
close($fh);
#Printing reactions
#As it stands, it's a copy of the master reactions file with the pathways, aliases, and ec numbers integrated
open(FH, "< ".$opt->reactions);
open($fh, ">", $directory."Reactions.tsv");
$header = 1;
undef(#headers);
my %Reactions=();
while(<FH>){
chomp;
if($header){
#headers = split(/\t/,$_,-1);
print $fh join("\t", grep { $_ ne 'is_obsolete' && $_ ne 'linked_reaction' } #headers),"\n";
$header--;
next;
}
#temp=split(/\t/,$_,-1);
#map values to keys
#probably not that necessary, but useful if column order changes
my %rxnHash=();
for(my $i=0;$i<scalar(#headers);$i++){
$rxnHash{$headers[$i]}=$temp[$i];
}
my #ecnums = ();
my #aliases = ();
foreach my $aliasSet (keys %{$alias_rxn_hash{$rxnHash{id}}}){
foreach my $alias (keys %{$alias_rxn_hash{$rxnHash{id}}{$aliasSet}}){
#Only include full ec numbers (?)
if ($aliasSet eq "Enzyme Class"){
if($alias =~ m/\d+\.\d+\.\d+\.\d+/){
push(#ecnums, $alias);
}
}else{
push(#aliases, "\"".$aliasSet.":".$alias."\"");
}
}
}
$rxnHash{aliases}= scalar(#aliases)>0 ? join(";",#aliases) : "null";
$rxnHash{ec_numbers}= scalar(#ecnums)>0 ? join(";",#ecnums) : "null";
my #pathways = ();
if (defined($rxn_pathways->{$rxnHash{id}})) {
foreach my $type (keys(%{$rxn_pathways->{$rxnHash{id}}})) {
foreach my $path (keys(%{$rxn_pathways->{$rxnHash{id}}{$type}})) {
push(#pathways, $type.":".$path);
}
}
}
$rxnHash{pathways}= scalar(#pathways)>0 ? join(";",#pathways) : "null";
print $fh join("\t", map { $rxnHash{$_} } grep { $_ ne 'is_obsolete' && $_ ne 'linked_reaction' } #headers),"\n";
$Reactions{$rxnHash{id}}=\%rxnHash;
}
close($fh);
#Printing template biomasses reactions
open($fh, ">", $directory."TemplateBiomasses.tsv");
$columns = [qw(
id
name
type
other
dna
rna
protein
lipid
cellwall
cofactor
energy
template_id
template_name
template_modeltype
template_domain
template_version
template_is_current
template_owner
compartment_ids
compound_ids
compound_data
)];
print $fh join("\t",#{$columns})."\n";
for (my $i=0; $i < #{$templates}; $i++) {
my $biomasses = $templates->[$i]->templateBiomasses();
for (my $j=0; $j < #{$biomasses}; $j++) {
my $compounds = {};
my $comps = {};
my $bio = $biomasses->[$j];
my $biocpds = $bio->templateBiomassComponents();
my #compounddata = ();
for (my $k=0; $k < #{$biocpds}; $k++) {
my $biocpd = $biocpds->[$k];
my $biocpd_id = $biocpd->compound()->id();
my #links = ();
my $linkrefs = $biocpd->linked_compounds();
for (my $m=0; $m < #{$linkrefs}; $m++) {
push(#links, $linkrefs->[$m]->id()."{".$biocpd->link_coefficients()->[$m]."}");
}
$compounds->{$biocpd_id} = 1;
$comps->{$biocpd->compartment()->id()} = 1;
push(#compounddata, $biocpd_id.":\"".$Compounds{$biocpd_id}{name}."\":".$biocpd->coefficient().":".$biocpd->coefficientType().":".$biocpd->class().":".join("|",#links));
}
my $data = [
$templatedata->[$i]->[0].".".$bio->id(),
$bio->name(),
"growth",
$bio->other(),
$bio->dna(),
$bio->rna(),
$bio->protein(),
$bio->lipid(),
$bio->cellwall(),
$bio->cofactor(),
$bio->energy(),
$templatedata->[$i]->[0],
$templatedata->[$i]->[1],
$templatedata->[$i]->[2],
$templatedata->[$i]->[3],
$templatedata->[$i]->[4],
$templatedata->[$i]->[5],
$templatedata->[$i]->[6],
"0:".join(";0:",keys(%{$comps})),
join(";",keys(%{$compounds})),
join(";",#compounddata)
];
print $fh join("\t",#{$data})."\n";
}
}
close($fh);
#Printing template reactions
open($fh, ">", $directory."TemplateReactions.tsv");
$columns = [qw(
id
reaction_id
abbreviation
name
code
stoichiometry
is_transport
equation
definition
model_direction
gapfill_direction
type
base_cost
forward_penalty
reverse_penalty
pathways
aliases
ec_numbers
deltag
deltagerr
template_id
template_name
template_modeltype
template_domain
template_version
template_is_current
template_owner
compartment_ids
complex_ids
compound_ids
)];
print $fh join("\t",#{$columns})."\n";
for (my $i=0; $i < #{$templates}; $i++) {
my $rxns = $templates->[$i]->templateReactions();
for (my $j=0; $j < #{$rxns}; $j++) {
my $rxn = $rxns->[$j];
my $complexes = {};
my $cpxs = $rxn->complexs();
for (my $j=0; $j < #{$cpxs}; $j++) {
$complexes->{$idhash->{$cpxs->[$j]->id()}} = 1;
}
my $compounds = {};
my $comps = {};
# my $rgts = [split(/;/,$Reactions{$rxn->reaction()->id()}{stoichiometry})];
my $rgts = $rxn->reaction()->reagents();
for (my $j=0; $j < #{$rgts}; $j++) {
# my ($coef,$cpd,$cmpt) = split(/:/,$rgts->[$j]);
my ($cpd,$cmpt) = ($rgts->[$j]->compound()->id(),$rgts->[$j]->compartment()->id());
$compounds->{$cpd}=1;
$comps->{$cmpt}=1;
}
my $rxn_id = $rxn->reaction()->id();
my $compid = "c0";
my $data = [
$templatedata->[$i]->[0].".".$rxn_id."_".$compid,
$rxn_id,
$Reactions{$rxn_id}{abbreviation}."_".$compid,
$Reactions{$rxn_id}{name}."_".$compid,
# $Reactions{$rxn_id}{code},
# $Reactions{$rxn_id}{stoichiometry},
$rxn->reaction()->code(),
$rxn->reaction()->stoichiometry(),
$Reactions{$rxn_id}{is_transport},
# $Reactions{$rxn_id}{equation},
# $Reactions{$rxn_id}{definition},
$rxn->reaction()->equation(),
$rxn->reaction()->definition(),
$rxn->direction(),
defined($rxn->GapfillDirection()) ? $rxn->GapfillDirection() : "=",
"null",
defined($rxn->base_cost()) ? $rxn->base_cost() : 0,
defined($rxn->forward_penalty()) ? $rxn->base_cost() : 0,
defined($rxn->reverse_penalty()) ? $rxn->base_cost() : 0,
$Reactions{$rxn_id}{pathways},
$Reactions{$rxn_id}{aliases},
$Reactions{$rxn_id}{ec_numbers},
$Reactions{$rxn_id}{deltag},
$Reactions{$rxn_id}{deltagerr},
$templatedata->[$i]->[0],
$templatedata->[$i]->[1],
$templatedata->[$i]->[2],
$templatedata->[$i]->[3],
$templatedata->[$i]->[4],
$templatedata->[$i]->[5],
$templatedata->[$i]->[6],
"0:".join(";0:",keys(%{$comps})),
join(";",keys(%{$complexes})),
join(";",keys(%{$compounds}))
];
print $fh join("\t",#{$data})."\n";
}
}
close($fh);

Answer 1

my $templates = [
$fba->_get_msobject("ModelTemplate","KBaseTemplateModels","GramPosModelTemplate"), ###line171
$fba->_get_msobject("ModelTemplate","KBaseTemplateModels","GramNegModelTemplate"), ###line172
$fba->_get_msobject("ModelTemplate","KBaseTemplateModels","CoreModelTemplate"), ###line173
$fba->_get_msobject("ModelTemplate","KBaseTemplateModels","PlantModelTemplate") ###line174
];
The code is calling a method on the object in $fba without first declaring it it or even assigning an object to it. (In Python terms, the code does fba._get_msobject(...) without first doing fba = ....)
Not only will you need to declare the variable (my $fba), you will need to assign to it whatever object it's supposed to have.