Initial commit
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Zhongwei Li
201
skills/editing-obo-ontologies/obo-checkin.pl
Executable file
201
skills/editing-obo-ontologies/obo-checkin.pl
Executable file
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#!/usr/bin/perl -w
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use strict;
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use FileHandle;
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my $outdir = "terms";
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my $cmd;
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my $dry_run = 0;
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my $preserve_files = 0;
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while ($ARGV[0] =~ /^\-/) {
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my $opt = shift @ARGV;
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if ($opt eq '-h' || $opt eq '--help') {
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print usage();
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exit 0;
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}
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if ($opt eq '-d' || $opt eq '--outdir') {
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$outdir = shift @ARGV;
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}
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if ($opt eq '-n' || $opt eq '--dry-run') {
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$dry_run = 1;
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}
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if ($opt eq '-p' || $opt eq '--preserve-files') {
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$preserve_files = 1;
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}
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}
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`mkdir -p $outdir`;
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my $id;
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my $stanza = "";
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my @alt_ids = ();
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my $fn = shift @ARGV;
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# ensure ids are sorted
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my @ids = sort @ARGV;
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my %new_stanza_map = ();
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foreach my $id (@ids) {
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my $path = get_path($id);
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# check if $id is a path to a file that exists
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if ($id =~ m@[\./]@ && -e $id) {
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open(F, $id) || die "no such file $id";
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my @lines = <F>;
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close(F);
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my $uber_stanza = join("", @lines);
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my @stanzas_in_block = split(/\n\n/, $uber_stanza);
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foreach my $stanza (@stanzas_in_block) {
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# trim whitespace
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$stanza =~ s/\s+$//;
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if (!length($stanza)) {
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next;
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}
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# check if stanza has id (note that stanza is multi-line)
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if ($stanza =~ /id:\s+(\S+)/) {
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my $stanza_id = $1;
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$new_stanza_map{$stanza_id} = "$stanza\n\n";
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}
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else {
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die "no id found in $stanza";
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}
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}
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}
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else {
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open(F, $path) || die "no such file $path";
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my $stanza = "";
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while(<F>) {
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chomp;
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$stanza .= "$_\n";
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}
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close(F);
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if ($stanza =~ /id: (\S+)/) {
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# check id matches
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if ($1 ne $id) {
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die "id mismatch $1 ne $id";
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}
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}
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else {
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die "no id found in $path";
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}
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$new_stanza_map{$id} = $stanza;
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}
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}
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open(W, ">$fn.tmp") || die "cannot write tp $fn.tmp";
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my %stanza_map = ();
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my %stanza_type_map = (); # To track stanza type (Term or Typedef)
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$/ = "\n\n";
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open(F, $fn) || die "cannot open $fn";
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while(<F>) {
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if ($_ =~ /id: (\S+)/) {
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my $id = $1;
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$stanza_map{$id} = $_;
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# Determine stanza type
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if ($_ =~ /\[(\w+)\]/) {
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$stanza_type_map{$id} = $1;
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}
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else {
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# Default to Term if type not specified
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$stanza_type_map{$id} = "Term";
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}
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}
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else {
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print W $_;
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}
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}
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close(F);
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# combine old and new stanzas
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foreach my $id (sort keys %new_stanza_map) {
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$stanza_map{$id} = $new_stanza_map{$id};
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# Update stanza type for new stanzas
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if ($new_stanza_map{$id} =~ /\[(\w+)\]/) {
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my $s = $1;
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$stanza_type_map{$id} = $s;
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}
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else {
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# Default to Term if type not specified
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$stanza_type_map{$id} = "Term";
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}
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}
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# Sort ids by stanza type (Term first, then Typedef) and then alphabetically within each type
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my @sorted_ids = sort {
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# First compare stanza types (Term comes before Typedef)
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my $type_compare = ($stanza_type_map{$a} eq "Typedef") <=> ($stanza_type_map{$b} eq "Typedef");
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# If same type, sort alphabetically by ID
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return $type_compare || $a cmp $b;
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} keys %stanza_map;
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foreach my $id (@sorted_ids) {
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my $s = $stanza_map{$id};
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# normalize line endings to strip trailing whitespace
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$s =~ s@[\r\n]+$@\n\n@;
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print W $s;
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}
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close(W);
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if ($dry_run) {
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print "dry run, no changes made\n";
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}
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else {
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`mv $fn.tmp $fn`;
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# clear out @ids from $outdir
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foreach my $id (@ids) {
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my $path = get_path($id);
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if (!$preserve_files) {
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unlink $path;
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}
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}
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}
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# get the path for an id
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# the ID should be either:
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# - an ontology curie, e.g. GO:0000001, in which case the path is terms/GO_0000001.obo
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# - an OWL local name, e.g. GO_0000001, in which case the path is terms/GO_0000001.obo
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# - a file name, e.g. terms/my_terms.obo, in which case the path is terms/my_terms.obo
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sub get_path {
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my ($id) = @_;
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my $fn = "$id";
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$fn =~ s@:@_@;
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# if the id has : or / in it and is a path to a file that exists, return it
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if ($fn =~ m@[\./]@ && -e $fn) {
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return $fn;
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}
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return "$outdir/$fn.obo"
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}
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sub w {
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my ($id, $stanza) = @_;
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my $path = get_path($id);
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open(F, ">$path") || die($path);
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print F $stanza;
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close(F)
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}
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sub scriptname {
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my @p = split(/\//,$0);
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pop @p;
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}
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sub usage {
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my $sn = scriptname();
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<<EOM;
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$sn OBO-FILE [ -d TERM-DIR ] TERM1 TERM2 ...
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Checks in obo files from TERM-DIR into the OBO-FILE
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Example:
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$sn src/ontology/foo-edit.obo FOO:0000087 FOO:0000081
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This will check in the FOO:0000087 and FOO:0000081 terms from the terms directory
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into the foo-edit.obo file.
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EOM
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}
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