# HG changeset patch
# User jade
# Date 1400713557 14400
# Node ID 27285b6627ef0da3c37b098e450ff5783c7f405f
# Parent  078e9ae01769d8f7ad6ac16fbfd956627125c0df
Deleted selected files

diff -r 078e9ae01769 -r 27285b6627ef abyss-pe_wrapper.pl
--- a/abyss-pe_wrapper.pl	Wed May 21 19:04:47 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,90 +0,0 @@
-#!/usr/bin/env perl
-
-use strict;
-use warnings;
-use File::Copy;
-
-die("ERROR: Expected at least 8 arguments; got: @ARGV\n") unless @ARGV >= 8;
-
-# GET ARGS
-my $kmer_size=shift @ARGV;
-my $min_num_pairs=shift @ARGV;
-my $outdir=shift @ARGV;
-my $outfile=shift @ARGV;
-my $contigs_outfile=shift @ARGV;
-my $sam_outfile=shift @ARGV;
-my $hist_outfile=shift @ARGV;
-
-# ALL FILES GO IN THIS extra_files_path
-unless (-d $outdir) {
-    mkdir $outdir or die("Unable to make dir, $outdir\n");
-}
-chdir $outdir;
-
-# RUN COMMAND
-`abyss-pe k=$kmer_size n=$min_num_pairs in='@ARGV' name=abyss 2> $outdir/abyss.stderr > $outdir/abyss.stdout`;
-if ($? != 0) {
-    unless ( -s "$outdir/abyss-3.hist") { print STDERR "NO CONTIGS WERE PRODUCED!\n" }
-    open(IN, "<$outdir/abyss.stdout") or die($!);
-    while (<IN>) { print STDERR $_ }
-    close IN;
-    die("ABORTING\n");
-}
-
-# FILTER HISTOGRAM
-open (IN, "<$outdir/abyss.stderr") or die($!);
-open (OUT, ">$outfile") or die($!);
-while (my $line=<IN>) {
-    my @chars=split(//, $line);
-    my $filter=0;
-    foreach my $char (@chars) {
-        if (ord($char) >= 129) {
-            $filter=1;
-            last;
-        }
-    }
-    print OUT $line unless $filter;
-}
-close IN;
-close OUT;
-unlink("$outdir/abyss.stderr");
-
-# OUTPUT INFO LINE TEXT
-open(IN, "<$outdir/abyss.stdout") or die($!);
-while (<IN>) {
-    if (/^Assembled \d+ k\-mer in \d+ contigs/) {
-        print;
-        last;
-    }
-}
-close IN;
-
-# GALAXY DOESN'T WANT GZIPPED DATAFILES
-run("gunzip $outdir/abyss-3.sam.gz");
-
-# MOVE OUTFILES
-mv_outfile("$outdir/abyss-contigs.fa", $contigs_outfile);
-mv_outfile("$outdir/abyss-3.sam", $sam_outfile);
-mv_outfile("$outdir/coverage.hist", $hist_outfile);
-exit;
-
-sub run {
-    my $cmd=shift;
-    my $output=`$cmd 2>&1`;
-    if ($? != 0) {
-        print STDERR "ERROR RUNNING COMMAND: $cmd\n";
-        die($output);
-    }
-    return $output;
-}
-
-
-sub mv_outfile {
-    my ($src,$dest)=@_;
-    # if dest defined and src exist, then move outfiles to galaxy-specified location
-    if ( $dest ne 'None' and -f $src ) {
-        unlink($dest);
-        move($src,$dest);
-    }
-}
-__END__