Topic/repetitive measurements2

bin/convert_ncsu_excel_to_obo.pl

@@ -0,0 +1,336 @@
+
+=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
+
+use strict;
+
+use utf8;
+use Getopt::Std;
+use Data::Dumper;
+use CXGN::File::Parse;
+
+our ($opt_n, $opt_i, $opt_o, $opt_h);
+
+getopts('n:i:o:h');
+
+my $file = $opt_i;
+my $ontology_name = $opt_n || "GENERIC";
+
+if (!$file) {
+    die "Please privde a file using the -i parameter.";
+}
+
+my $outfile = $file.".obo";
+my $cvpropfile = $file.".props";
+
+open(my $F, ">", $outfile) || die "Can't open file $outfile\n";
+open(my $G, ">", $cvpropfile) || die "Can't open cvprop file $cvpropfile for writing";
+
+#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
+
+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" );
+
+# 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";
+
+my $parser = CXGN::File::Parse->new( file => $file );
+
+my $parsed = $parser->parse();
+
+if ($parsed->{errors}) {
+    warn "The following errors occurred while parsing file $file: ".Dumper($parsed->{errors})."\n";
+}
+
+my $data = $parsed->{data};
+
+# get all the trait classes
+#
+my %trait_classes;
+my %traits;
+my %variables;
+
+foreach my $d (@$data) {
+    $trait_classes{$d->{$trait_class}}->{count}++;
+}
+print STDERR "TRAIT CLASSES: ".Dumper(\%trait_classes);
+
+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};
+
+    print STDERR "TRAIT NAME $trait_name has TRAIT CLASS $d->{$trait_class}\n";
+
+    $traits{$tn}->{$trait_definition} = $d->{$trait_definition};
+}
+
+print STDERR "TRAITS: ".Dumper(\%traits);
+
+
+
+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);
+
+
+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
+
+print STDERR "Starting at term $ontology_name:$acc ...\n";
+
+# 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
+
+# write cvprops header
+#
+print $G join("\t", "trait_name", "trait_format", "trait_default_value", "trait_minimum", "trait_maximum", "trait_categories", "trait_details")."\n";
+
+
+# read header
+#
+my $header = <$F>;
+
+my $root_acc = $acc;
+my $root_name = "ROOT";
+
+print $F <<TERM;
+
+[Term]
+id: $ontology_name:$acc
+name: ROOT
+namespace: $ontology_name
+
+TERM
+
+
+$count++;
+
+foreach my $k (sort keys %trait_classes) {
+
+    print $F format_trait(
+	$ontology_name,
+	$class_id,
+	$class_name,
+	$class_name,
+	undef,
+	$ontology_name,
+	$root_name,
+	)."\n";
+
+    $trait_classes{$k}->{acc} = $class_id;
+    #$trait_classes{$k}->{name} = $k;
+
+    $count++;
+
+}
+
+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";
+
+    $traits{$k}->{name} = $traits{$k}->{$trait_name};
+    $traits{$k}->{acc} = $traits{$k}->{$trait_id};
+    $count++;
+}
+
+
+
+foreach my $k (sort keys %variables) { 
+
+    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};
+
+    print STDERR "VARIABLE: $k. PARENT TRAIT: $parent_trait\n";
+
+    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
+
+	)."\n";
+
+    print $G format_props(
+	$k, # variable name
+	$ontology_name,
+	$count,
+	$variables{$k}->{'Scale class'},
+	$variables{$k}->{Categories},
+	);
+
+    $count++;
+
+}
+
+close($F);
+close($G);
+
+print STDERR "Script completed.\n";
+
+sub format_props {
+    my $trait_name = shift;
+    my $ontology_name = shift;
+    my $count = shift;
+    my $trait_format = shift;
+    my $categories = shift;
+
+    my $trait_default_value = shift;
+    my $trait_minimum = shift;
+    my $trait_maximum = shift;
+    my $trait_details = shift;
+
+    return join ("\t", $trait_name."|".format_ontology_id($ontology_name, $count), $trait_format, $trait_default_value, $trait_minimum, $trait_maximum, $categories, $trait_details)."\n";
+
+
+}
+
+
+sub format_ontology_id {
+    my $ontology_name = shift;
+    my $acc = shift;
+
+    return $ontology_name.":".sprintf "%07d", $acc;
+}
+
+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;
+
+    my $trait_id = format_ontology_id($ontology_code, $id);
+    my $parent_trait_id = format_ontology_id($ontology_code, $parent_class_id);
+
+    my %record = (
+	"[Term]" => "",
+	"id:" =>  $trait_id,
+	"name:" =>  $name,
+	"def:" => "\"$description\" []",
+	"synonym:" => $synonyms,
+	"namespace:" => $ontology_name,
+	"is_a:" => "$parent_trait_id ! $parent_trait",
+	);
+
+    my $data = "";
+    foreach my $k ("[Term]", "id:", "name:", "def:", "synonym:", "namespace:", "is_a:") {
+	if (defined($record{$k})) {
+	    $data .= "$k $record{$k}\n";
+	}
+    }
+
+    return $data;
+}
+
+
+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;
+
+    #print STDERR "Parent trait name: $parent_trait_name\n";
+
+    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",
+	);
+
+    my $data = "";
+    foreach my $k ("[Term]", "id:", "name:", "def:", "synonym:", "namespace:", "relationship:") {
+	if (defined($record{$k})) {
+	    $data .= "$k $record{$k}\n";
+	}
+    }
+
+    return $data;
+}

bin/load_trait_props.pl

@@ -28,18 +28,21 @@ =head2 DESCRIPTION
   trait_maximum
   trait_categories
   trait_details
+  trait_repeat_type
 
   trait_name: the name of the variable human readable form (e.g., "plant height in cm")
   trait_format: can be numeric, qualitative, date or boolean
   trait_default_value: is the value if no value is given
   trait_categories: are the different possible names of the categories, separated by /, for example "1/2/3/4/5"
   trait_details: string describing the trait categories 
+  trait_repeat_type: one of 'single', 'multiple', 'time_series'
 
 =head2 AUTHOR
 
-Jeremy D. Edwards ([email protected])
+ Jeremy D. Edwards ([email protected]) - initial script, April 2014
+ Lukas Mueller ([email protected]) - added trait_repeat_type, Feb 2024
+
 
-April 2014
 
 =head2 TODO