Perl 오류-전역 기호에는 명시적인 패키지 이름이 필요합니다.

실행해야하는 Perl 파일을 실행하는 동안 오류가 발생합니다. (보통 Python을 사용하지만 Perl을 포함한 다른 프로그래밍 언어를 모릅니다.) 먼저 오류를 표시하고 마지막에 전체 코드를 첨부합니다.

오류:

$ 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.

오류에 언급 된 전역 기호 앞에 "my"를 입력하면 이번에는 아래에 또 다른 오류가 발생합니다.

$ 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.

그래서 지금은 어떻게해야할지 모르겠습니다. 이 Perl 스크립트는 "ComplexRoles.tsv"및 "TemplateReactions.tsv"라는 두 개의 필수 파일을 덤프 / 추출합니다.

Python 3.7과 Cygwin64를 사용하고 있습니다. ModelSEEDDatabase Github 링크 : https://github.com/ModelSEED/ModelSEEDDatabase

도와 주시면 정말 기쁩니다. 미리 감사드립니다.

전체 스크립트는 다음과 같습니다. (문제가있는 줄은 171, 172, 173, 174, 202, 233입니다.)

#!/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);