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| =head1 NAME | ||
| convert_excel_to_obo - a script to convert a spreadsheet based representation of an ontology to an obo file format | ||
| =head1 DESCRIPTION | ||
| Based on CXGN::File::Parse, this script can parse tab delimited or Excel formats (xls or xlsx) as follows: | ||
| perl convert_excel_to_obo.pl -n CO_999 -i file.xlsx -o ontology.obo | ||
| =head1 AUTHOR | ||
| Lukas Mueller <[email protected]> | ||
| October 2024 | ||
| =cut | ||
|
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| use strict; | ||
|
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| use utf8; | ||
| use Getopt::Std; | ||
| use Data::Dumper; | ||
| use CXGN::File::Parse; | ||
|
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| our ($opt_n, $opt_i, $opt_o, $opt_h); | ||
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| getopts('n:i:o:h'); | ||
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| my $file = $opt_i; | ||
| my $ontology_name = $opt_n || "GENERIC"; | ||
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| if (!$file) { | ||
| die "Please privde a file using the -i parameter."; | ||
| } | ||
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| my $outfile = $file.".obo"; | ||
| my $cvpropfile = $file.".props"; | ||
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| open(my $F, ">", $outfile) || die "Can't open file $outfile\n"; | ||
| open(my $G, ">", $cvpropfile) || die "Can't open cvprop file $cvpropfile for writing"; | ||
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| #Curation Variable ID Variable name Variable label Variable description Variable synonyms Context of use Growth stage Variable status Variable Xref Institution Scientist Date Language Crop Trait ID Entity Attribute Trait name Trait class Trait description Trait synonyms Main trait abbreviation Alternative trait abbreviations Trait status Trait Xref Method ID Method name Method class Method description Method Abbreviation Formula Method reference Scale ID Scale name Scale Abbreviation Scale class Scale Xref Cat 1 code Cat 1 description Cat 2 code Cat 2 description Cat 3 code Cat 3 description Cat 4 code Cat 4 description Cat 5 code Cat 5 description Cat 6 code Cat 6 description Cat 7 code Cat 7 description Cat 8 code Cat 8 description Cat 9 code Cat 9 description Cat 10 code Cat 10 description | ||
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| my @col_headers = ("Variable"," Term Name - BB", "Trait class", "Term Definition", "Variable Full Name", "Synonyms", "Trait - CO", "Main trait abbreviation", "Entity", "Attribute", "Method Name", "Method class", "Method description", "Method Abbreviation", "Formula", "Scale name", "Scale abbreviation", "Scale class", "Category 1", "Category 2", "Category 3", "Category 4", "Category 5", "Category 6", "Category 7", "Category 8", "Category 9", "Category 10", "Category 11", "Category 12" ); | ||
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| # column labels | ||
| # | ||
| my $trait_class = "Trait class"; | ||
| my $trait_name = "Trait name"; | ||
| my $trait_definition = "Trait description"; | ||
| my $trait_synonyms = "Trait synonyms"; | ||
| my $variable_synonyms = "Variable synonyms"; | ||
| my $trait_id = "Trait ID"; | ||
| my $variable_name = "Variable name"; | ||
| my $variable_definition = "Variable description"; | ||
| my $variable_label = "Variable label"; | ||
| my $variable_id = "Variable ID"; | ||
| my $method_id = "Method ID"; | ||
| my $method_name = "Method name"; | ||
| my $method_class = "Method class"; | ||
| my $method_description = "Method description"; | ||
| my $scale_id = "Scale ID"; | ||
| my $scale_name = "Scale name"; | ||
| my $scale_class = "Scale class"; | ||
| my $scale_description = "Scale description"; | ||
| my $scale_abbreviation = "Scale abbreviation"; | ||
| my $entity = "Entity"; | ||
| my $attribute = "Attribute"; | ||
| my $categories = "Categories"; | ||
| my $class_id = "Class ID"; | ||
| my $class_name = "Class name"; | ||
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| my $parser = CXGN::File::Parse->new( file => $file ); | ||
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| my $parsed = $parser->parse(); | ||
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| if ($parsed->{errors}) { | ||
| warn "The following errors occurred while parsing file $file: ".Dumper($parsed->{errors})."\n"; | ||
| } | ||
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| my $data = $parsed->{data}; | ||
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| # get all the trait classes | ||
| # | ||
| my %trait_classes; | ||
| my %traits; | ||
| my %variables; | ||
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| foreach my $d (@$data) { | ||
| $trait_classes{$d->{$trait_class}}->{count}++; | ||
| } | ||
| print STDERR "TRAIT CLASSES: ".Dumper(\%trait_classes); | ||
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| foreach my $d (@$data) { | ||
| my $tn = $d->{$trait_name}; | ||
| print STDERR "Parsing TRAIT NAME $trait_name\n"; | ||
| if (! $tn) { next; } | ||
| $traits{$tn}->{$trait_id} = $d->{$trait_id}; | ||
| $traits{$tn}->{$trait_class} = $d->{$trait_class}; | ||
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| print STDERR "TRAIT NAME $trait_name has TRAIT CLASS $d->{$trait_class}\n"; | ||
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| $traits{$tn}->{$trait_definition} = $d->{$trait_definition}; | ||
| } | ||
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| print STDERR "TRAITS: ".Dumper(\%traits); | ||
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| foreach my $d (@$data) { | ||
| my $vn = $d->{$variable_name}; | ||
| if (! $vn) { next; } | ||
| $variables{$vn}->{$variable_id} = $d->{$variable_id}; | ||
| $variables{$vn}->{$variable_synonyms} = $d->{$variable_synonyms}; | ||
| $variables{$vn}->{$trait_name} = $d->{$trait_name}; | ||
| $variables{$vn}->{$trait_definition} = $d->{$trait_definition}; | ||
| $variables{$vn}->{$entity} = $d->{$entity}; | ||
| $variables{$vn}->{$attribute} = $d->{$attribute}; | ||
| $variables{$vn}->{$method_name} = $d->{$method_name}; | ||
| $variables{$vn}->{$scale_abbreviation} = $d->{$scale_abbreviation}; | ||
| $variables{$vn}->{$variable_label} = $d->{$variable_label}; | ||
| $variables{$vn}->{$scale_name} = $d->{$scale_name}; | ||
| $variables{$vn}->{$scale_class} = $d->{$scale_class}; | ||
| $variables{$vn}->{$categories} = $d->{$categories}; | ||
| print STDERR "TERM NAME - CO IN variable = $d->{$trait_name}\n"; | ||
| $variables{$vn}->{$trait_name} = $d->{$trait_name}; | ||
| } | ||
| print STDERR "VARIABLES: ".Dumper(\%variables); | ||
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| my $root_id = format_ontology_id($opt_n, 0); | ||
| my $count = $root_id; | ||
| my $acc = sprintf "%07d", $count; # the number after the ontology name and a colon | ||
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| print STDERR "Starting at term $ontology_name:$acc ...\n"; | ||
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| # write obo header | ||
| # | ||
| print $F <<HEADER; | ||
| format-version: 1.2 | ||
| date: 10:03:2024 17:10 | ||
| saved-by: Lukas_Mueller | ||
| default-namespace: $ontology_name | ||
| ontology: CO_365 | ||
| HEADER | ||
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| # write cvprops header | ||
| # | ||
| print $G join("\t", "trait_name", "trait_format", "trait_default_value", "trait_minimum", "trait_maximum", "trait_categories", "trait_details")."\n"; | ||
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| # read header | ||
| # | ||
| my $header = <$F>; | ||
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| my $root_acc = $acc; | ||
| my $root_name = "ROOT"; | ||
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| print $F <<TERM; | ||
| [Term] | ||
| id: $ontology_name:$acc | ||
| name: ROOT | ||
| namespace: $ontology_name | ||
| TERM | ||
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| $count++; | ||
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| foreach my $k (sort keys %trait_classes) { | ||
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| print $F format_trait( | ||
| $ontology_name, | ||
| $class_id, | ||
| $class_name, | ||
| $class_name, | ||
| undef, | ||
| $ontology_name, | ||
| $root_name, | ||
| )."\n"; | ||
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| $trait_classes{$k}->{acc} = $class_id; | ||
| #$trait_classes{$k}->{name} = $k; | ||
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| $count++; | ||
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| } | ||
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| foreach my $k (sort keys %traits) { | ||
| print $F format_trait( | ||
| $ontology_name, | ||
| $traits{$k}->{$trait_id}, | ||
| $traits{$k}->{$variable_name}, | ||
| $traits{$k}->{$trait_definition}, | ||
| $traits{$k}->{$trait_synonyms}, | ||
| $trait_classes{ $traits{$k}->{$trait_class} }->{acc}, # parent id | ||
| $traits{$k}->{$trait_class}, # parent trait | ||
| )."\n"; | ||
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| $traits{$k}->{name} = $traits{$k}->{$trait_name}; | ||
| $traits{$k}->{acc} = $traits{$k}->{$trait_id}; | ||
| $count++; | ||
| } | ||
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| foreach my $k (sort keys %variables) { | ||
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| my $parent_trait = $variables{$k}->{$trait_name}; | ||
| my $parent_trait_id = $traits{$variables{$k}->{'Trait - CO'}}->{acc}; | ||
| my $parent_trait_name = $traits{ $variables{$k}->{'Trait -CO'}}->{name}; | ||
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| print STDERR "VARIABLE: $k. PARENT TRAIT: $parent_trait\n"; | ||
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| print $F format_variable( | ||
| $ontology_name, | ||
| $count, | ||
| $k, ###$variables{$k}->{'Variable Full Name'}, | ||
| join(" - ", $variables{$k}->{'Term Definition'}), | ||
| $variables{$k}->{'Synonym'}, | ||
| $traits{$variables{$k}->{'Trait - CO'}}->{acc}, # parent trait id | ||
| $traits{$variables{$k}->{'Trait - CO'}}->{name}, # parent trait | ||
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| )."\n"; | ||
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| print $G format_props( | ||
| $k, # variable name | ||
| $ontology_name, | ||
| $count, | ||
| $variables{$k}->{'Scale class'}, | ||
| $variables{$k}->{Categories}, | ||
| ); | ||
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| $count++; | ||
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| } | ||
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| close($F); | ||
| close($G); | ||
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| print STDERR "Script completed.\n"; | ||
|
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| sub format_props { | ||
| my $trait_name = shift; | ||
| my $ontology_name = shift; | ||
| my $count = shift; | ||
| my $trait_format = shift; | ||
| my $categories = shift; | ||
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| my $trait_default_value = shift; | ||
| my $trait_minimum = shift; | ||
| my $trait_maximum = shift; | ||
| my $trait_details = shift; | ||
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| return join ("\t", $trait_name."|".format_ontology_id($ontology_name, $count), $trait_format, $trait_default_value, $trait_minimum, $trait_maximum, $categories, $trait_details)."\n"; | ||
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| } | ||
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|
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| sub format_ontology_id { | ||
| my $ontology_name = shift; | ||
| my $acc = shift; | ||
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| return $ontology_name.":".sprintf "%07d", $acc; | ||
| } | ||
|
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| sub format_trait { | ||
| my $ontology_code = shift; | ||
| my $id = shift; | ||
| my $name = shift; | ||
| my $description = shift; | ||
| my $synonyms = shift; | ||
| my $parent_class_id = shift; | ||
| my $parent_trait = shift; | ||
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| my $trait_id = format_ontology_id($ontology_code, $id); | ||
| my $parent_trait_id = format_ontology_id($ontology_code, $parent_class_id); | ||
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| my %record = ( | ||
| "[Term]" => "", | ||
| "id:" => $trait_id, | ||
| "name:" => $name, | ||
| "def:" => "\"$description\" []", | ||
| "synonym:" => $synonyms, | ||
| "namespace:" => $ontology_name, | ||
| "is_a:" => "$parent_trait_id ! $parent_trait", | ||
| ); | ||
|
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| my $data = ""; | ||
| foreach my $k ("[Term]", "id:", "name:", "def:", "synonym:", "namespace:", "is_a:") { | ||
| if (defined($record{$k})) { | ||
| $data .= "$k $record{$k}\n"; | ||
| } | ||
| } | ||
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| return $data; | ||
| } | ||
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| sub format_variable { | ||
| my $ontology_code = shift; | ||
| my $id = shift; | ||
| my $name = shift; | ||
| my $description = shift; | ||
| my $synonyms = shift; | ||
| my $parent_trait_id = shift; | ||
| my $parent_trait_name = shift; | ||
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| #print STDERR "Parent trait name: $parent_trait_name\n"; | ||
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| my $variable_id = format_ontology_id($ontology_code, $id); | ||
| my $parent_trait_id = format_ontology_id($ontology_code, $parent_trait_id); | ||
| my %record = ( | ||
| "[Term]" => "", | ||
| "id:" => $variable_id, | ||
| "name:" => $name, | ||
| "def:"=> "\"$description\" []", | ||
| "synonym:" => $synonyms, | ||
| "namespace:" => $ontology_name, | ||
| "relationship:" => "variable_of $parent_trait_id ! $parent_trait_name", | ||
| ); | ||
|
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| my $data = ""; | ||
| foreach my $k ("[Term]", "id:", "name:", "def:", "synonym:", "namespace:", "relationship:") { | ||
| if (defined($record{$k})) { | ||
| $data .= "$k $record{$k}\n"; | ||
| } | ||
| } | ||
|
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| return $data; | ||
| } |
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