Previous changeset 0:078e9ae01769 (2014-05-21) |
Commit message:
Deleted selected files |
removed:
abyss-pe_wrapper.pl |
b |
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 |
b |
@@ -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__ |