Initial commit

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

@@ -0,0 +1,113 @@
+#!/usr/bin/perl -w
+
+use strict;
+my %tag_h=();
+my $regexp = '';
+my $noheader;
+my $negate;
+my $count;
+my $idfile;
+while ($ARGV[0] =~ /^\-.+/) {
+    my $opt = shift @ARGV;
+    if ($opt eq '-h' || $opt eq '--help') {
+        print usage();
+        exit 0;
+    }
+    if ($opt eq '-r' || $opt eq '--regexp') {
+        $regexp = shift @ARGV;
+    }
+    if ($opt eq '--regexp-file') {
+        my $f = shift @ARGV;
+        my @or = ();
+        open(F,$f);
+        while(<F>) {
+            chomp;
+            push(@or,$_);
+        }
+        close(F);
+        $regexp = sprintf('id: (%s)\n', join('|',@or));
+    }
+    if ($opt eq '-c' || $opt eq '--count') {
+        $count = 1;
+    }
+    if ($opt eq '--noheader') {
+        $noheader = 1;
+    }
+    if ($opt eq '--idfile') {
+        my $idfile = shift;
+        open(F,$idfile) || die $idfile;
+        my @ids = ();
+        while(<F>) {
+            chomp;
+            s@\s.*@@;
+            push(@ids, $_);
+        }
+        close(F);
+        $regexp = "id: (" .  join("|", @ids) . ")\n";
+    }
+    if ($opt eq '-v' || $opt eq '--neg') {
+        $negate = 1;
+    }
+}
+
+
+$/ = "\n\n";
+
+my $n = 0;
+while (@ARGV) {
+    my $f = pop @ARGV;
+    if ($f eq '-') {
+        *F=*STDIN;
+    }
+    else {
+        open(F,$f) || die "cannot open $f";
+    }
+    my $hdr = 0;
+    while(<F>) {
+        if (!$hdr && $_ !~ /^\[/) {
+            print unless $noheader || $count;
+            $hdr = 1;
+        }
+        else {
+            if ($negate) {
+                if ($_ !~ /$regexp/) {
+                    $n++;
+                    print unless $count;
+                }
+            }
+            else {
+                if (/$regexp/) {
+                    $n++;
+                    print unless $count;
+                }
+            }
+        }
+    }
+}
+if ($count) {
+    print "$n\n";
+}
+
+exit 0;
+
+sub scriptname {
+    my @p = split(/\//,$0);
+    pop @p;
+}
+
+
+sub usage {
+    my $sn = scriptname();
+
+    <<EOM;
+$sn [--noheader] [--neg] [--r REGULAR-EXPRESSION] [--regexp-file FILE] OBO-FILE
+
+filters out stanzas from obo files
+
+Example:
+
+$sn -r 'def:.*transcript' go.obo
+
+EOM
+}
+