# HG changeset patch
# User Edward Kirton <eskirton@lbl.gov>
# Date 1346353107 25200
# Node ID 376092ae10ed9fbceeeb001becf2172b629f331d
# Parent  66f8262e1686d258e9e575bc0896a1471a3cd273
reformat output to tabular

diff -r 66f8262e1686 -r 376092ae10ed hmmer.xml
--- a/hmmer.xml	Mon Mar 05 22:51:04 2012 -0800
+++ b/hmmer.xml	Thu Aug 30 11:58:27 2012 -0700
@@ -1,8 +1,12 @@
 <tool id="hmmer" name="hmmer" version="1.0.0">
 <description>hmmscan/search seqs vs profiles</description>
-<command>
+<requirements>
+    <requirement type="package">hmmer</requirement>
+</requirements>
+<command interpreter="perl">
+hmmer_wrapper.pl
 $program
-##--cpu 8
+--cpu 8
 --tblout $tblout
 --domtblout $domtblout
 $acc
@@ -126,10 +130,6 @@
     <data name="tblout" format="tabular" label="${tool.name} on $on_string: Per-sequence hits" />
     <data name="domtblout" format="tabular" label="${tool.name} on $on_string: Per-domain hits" />
 </outputs>
-<requirements>
-    <requirement type="binary">hmmscan</requirement>
-    <requirement type="binary">hmmsearch</requirement>
-</requirements>
 <tests>
 </tests>
 <help>
diff -r 66f8262e1686 -r 376092ae10ed hmmer_wrapper.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hmmer_wrapper.pl	Thu Aug 30 11:58:27 2012 -0700
@@ -0,0 +1,39 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+use File::Copy;
+
+my $cmd="@ARGV";
+my ($tblout,$domtblout);
+die("Missing --tblout\n") unless $cmd =~ / \-\-?tblout\s+(\S+)/;
+$tblout = $1;
+die("Missing --domtblout\n") unless $cmd =~ / \-\-?domtblout\s+(\S+)/;
+$domtblout = $1;
+my $output = `$cmd 2>&1`;
+die("HMMer failure: $output\n") unless $? == 0;
+reformat($tblout);
+reformat($domtblout);
+exit;
+
+sub reformat
+{
+    my $infile = shift;
+    my $outfile = "$infile.new";
+    open(IN, "<$infile") or die($!);
+    open(OUT, ">$outfile") or die($!);
+    print OUT "#target name\taccession\tquery name\taccession\tE-value (full)\tscore (full)\tbias (full)\tE-value (best)\tscore (best)\tbias (best)\texp\treg\tclu\tov\tenv\tdom\trep\tinc\tdescription of target\n";
+    while (<IN>)
+    {
+        next if /^#/;
+        my @row0 = split(/\s+/);
+        my @row = @row0[0..17];
+        push @row, join(' ', @row0[18..$#row0]);
+        print OUT join("\t", @row), "\n";
+    }
+    close(IN);
+    close(OUT);
+    move($outfile,$infile);
+}
+
+__END__