Add bin/extract_taxid.pl

dbcls · Oct 17, 2024 · 6a7a9cb · 6a7a9cb
1 parent 755d0b2
commit 6a7a9cb
Showing 1 changed file with 40 additions and 0 deletions.
diff --git a/bin/extract_taxid.pl b/bin/extract_taxid.pl
@@ -0,0 +1,40 @@
+#!/usr/bin/perl -w
+use strict;
+use File::Basename;
+use Getopt::Std;
+my $PROGRAM = basename $0;
+my $USAGE=
+"Usage: $PROGRAM
+";
+
+my %OPT;
+getopts('', \%OPT);
+
+my %HASH;
+while (<>) {
+    chomp;
+    if (/^#/) {
+        next;
+    }
+
+    my @f = split(/\t/, $_, -1);
+    if (@f != 5) {
+        die;
+    }
+
+    if ($f[0] !~ /^\d+$/) {
+        die;
+    }
+    my $taxid1 = $f[0];
+    $HASH{$taxid1} = 1;
+
+    if ($f[2] ne "Ortholog") {
+        die;
+    }
+    my $taxid2 = $f[3];
+    $HASH{$taxid2} = 1;
+}
+
+for my $taxid (sort {$a <=> $b} keys %HASH) {
+    print "$taxid\n";
+}