diff hmmpress_wrapper.pl @ 0:c16d8db9338a

init repo

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hmmpress_wrapper.pl	Mon Mar 05 22:43:09 2012 -0800
@@ -0,0 +1,39 @@
+#!/usr/bin/perl
+
+use warnings;
+use strict;
+
+die("Infile, outfile, outdir required\n") unless @ARGV == 3;
+my ($infile, $outfile, $outdir)=@ARGV;
+
+# setup
+-d $outdir or mkdir($outdir) or die($!);
+symlink($infile,"$outdir/hmm");
+
+# create output header file
+open(IN, "<$infile") or die($!);
+open(OUT, ">$outfile") or die($!);
+my $ok=0;
+while (my $line=<IN>) {
+    if (!$ok) {
+        die("Invalid input file (HMMER3 format required)\n") unless $line =~ /^HMMER3/;
+        $ok=1;
+    } elsif ($line =~ /^HMM/) {
+        last;
+    } else {
+        print OUT $line;
+    }
+}
+close IN;
+close OUT;
+
+# hmmpress
+my $output=`hmmpress $outdir/hmm 2>&1`;
+if ($? != 0) {
+    $output="FAILED\n" unless $output;
+    die($output);
+}
+unlink("$outdir/hmm");
+my @output=split(/\n/, $output);
+print $output[1], "\n";
+exit;