Initial commit

skills/editing-obo-ontologies/obo-checkout.pl

@@ -0,0 +1,94 @@
+#!/usr/bin/perl -w
+
+use strict;
+use FileHandle;
+my $outdir = "terms";
+my $cmd;
+while ($ARGV[0] =~ /^\-/) {
+    my $opt = shift @ARGV;
+    if ($opt eq '-h' || $opt eq '--help') {
+        print usage();
+        exit 0;
+    }
+    if ($opt eq '-d' || $opt eq '--outdir') {
+        $outdir = shift @ARGV;
+    }
+}
+`mkdir -p $outdir`;
+my $id;
+my $stanza = "";
+my @alt_ids = ();
+my $fn = shift @ARGV;
+my @ids = @ARGV;
+my %idmap = map {$_ => 1} @ids;
+my $num_ids = scalar(@ids);
+
+my $n = 0;
+print "Reading $fn\n";
+open(F, $fn) || die "no such file $fn";
+while(<F>) {
+    if (m@^\[@) {
+        $n++;
+        if ($id) {
+            # check if id is in %idmap
+            if ($idmap{$id}) {
+                w($id, $stanza);
+            }
+        }
+        $stanza = "";
+        $id = "";
+    }
+    if (m@^id: (\S+)@) {
+        $id = $1;
+    }
+    if (m@^alt_id: (\S+)@) {
+        push(@alt_ids, $1);
+    }
+    $stanza .= $_;
+}
+close(F);
+#print "n: $n\n";
+sub get_path {
+    my ($id) = @_;
+    my $fn = "$id";
+    $fn =~ s@:@_@;
+    return "$outdir/$fn.obo"
+    
+}
+
+sub w {
+    my ($id, $stanza) = @_;
+    my $path = get_path($id);
+    print "Checking out $id to $path\n";
+    open(W, ">$path") || die($path);
+    print W $stanza;
+    close(W)
+}
+
+sub scriptname {
+    my @p = split(/\//,$0);
+    pop @p;
+}
+
+
+sub usage {
+    my $sn = scriptname();
+
+    <<EOM;
+$sn  OBO-FILE [ -d TERM-DIR ] TERM1 TERM2 ...
+
+Checks out obo files into TERM-DIR from the OBO-FILE
+
+Example:
+
+$sn src/ontology/foo-edit.obo FOO:0000087 FOO:0000081
+
+This will extract the FOO:0000087 and FOO:0000081 terms from the foo-edit.obo file
+and write them to the terms directory, as files:
+
+terms/FOO_0000087.obo
+terms/FOO_0000081.obo
+
+EOM
+}
+