diff kmernator_wrapper.pl @ 0:d9da256384e1 default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kmernator_wrapper.pl	Thu Jul 14 22:19:53 2011 -0400
@@ -0,0 +1,87 @@
+#!/usr/bin/env perl
+
+# FilterReads (AKA Kmernator) wrapper for Galaxy.
+# Kmernator by Rob Egan ([e-mail])
+# Wrapper for Galaxy supported by Edward Kirton ([e-mail])
+# Produced under funding from the United States Department of Energy Office of Science
+# Freely distributable under the same license as Galaxy itself.
+
+use strict;
+use warnings;
+use File::Copy;
+
+# SHIFT OUTFILE PATHS OFF ARGV
+die unless @ARGV;
+my $id=shift @ARGV;
+my $results_dir=shift @ARGV;
+my $working_dir=shift @ARGV;
+my $mmap_infile=shift @ARGV;
+my $kmer=shift @ARGV;
+my $mmap_outfile=shift @ARGV;
+my $gc_map_outfile=shift @ARGV;
+my $partition_by_depth=shift @ARGV;
+my $format=shift @ARGV;
+my @infiles=();
+my @history_ids=();
+while (my $infile=shift @ARGV) {
+    last if $infile eq 'END';
+    push @infiles, $infile;
+    my $hid=shift @ARGV;
+    push @history_ids, $hid;
+    die("Input file $hid does not exist ($infile)\n") unless -e $infile;
+}
+
+# PREPARE
+mkdir($working_dir) unless -d $working_dir;
+chdir($working_dir) or die($!);
+for (my $i=0; $i<=$#infiles; $i++) {
+    my $infile=$infiles[$i];
+    symlink($infile,"$working_dir/$i.fastq");
+    unshift @ARGV, "--input-file $working_dir/$i.fastq";
+}
+if ($mmap_infile ne 'None') {
+    symlink("$mmap_infile", "$working_dir/out-mmap");
+    unshift @ARGV, "--load-kmer-mmap 1";
+}
+
+# RUN
+my $output=`FilterReads @ARGV --output-file $working_dir/out`;
+die("Kmernator died while running command: @ARGV\nOUTPUT:\n$output\n") if $?;
+
+# MOVE OUTFILES
+if ($kmer < 1) {
+    my $dest=join("_",'primary',$id,'FilteredReads','visible',$format); 
+    move("out-in.fastq","$results_dir/$dest") or die($!);
+} elsif ($partition_by_depth > 0) {
+    opendir(DIR, $working_dir) or die($!);
+    my @files = readdir(DIR);
+    closedir(DIR);
+    foreach my $file ( @files ) {
+        next unless $file =~ /^out\-(MinDepth\d+\-PartitionDepth\d+)\.fastq$/ or $file =~ /^out\-(MinDepth\d+\-PartitionDepth\d+\-consensus\-\d+)\.fastq$/;
+        #next unless $file =~ /^out\-(MinDepth\d+\-PartitionDepth\d+)\-dataset_\d+\.fastq$/ or $file =~ /^out\-(MinDepth\d+\-PartitionDepth\d+\-consensus\-\d+)\.fastq$/;
+        my $dest=join("_",'primary',$id,$1,'visible',$format); 
+        move($file,"$results_dir/$dest") or die($!);
+    }
+    move("out-GC.txt",$gc_map_outfile) or die($!);
+    move("out-mmap",$mmap_outfile) or die($!);
+} else {
+    opendir(DIR, $working_dir) or die($!);
+    my @files = readdir(DIR);
+    closedir(DIR);
+    foreach my $file ( @files ) {
+        next unless $file =~ /^out\-(MinDepth\d+)\.fastq$/ or $file =~ /^out\-(MinDepth\d+\-consensus\-\d+)\.fastq$/;
+        #next unless $file =~ /^out\-(MinDepth\d+)\-dataset_\d+\.fastq$/ or $file =~ /^out\-(MinDepth\d+\-consensus\-\d+)\.fastq$/;
+        my $dest=join("_",'primary',$id,$1,'visible',$format); 
+        move($file,"$results_dir/$dest") or die($!);
+    }
+    move("out-GC.txt",$gc_map_outfile) or die($!);
+    move("out-mmap",$mmap_outfile) or die($!);
+}
+if ( -f "out-0-Artifact.fastq" ) {
+    for (my $i=0; $i<=$#infiles; $i++) {
+        my $hid=$history_ids[$i];
+        my $dest=join("_",'primary',$id,"Dataset-$hid-Artifact",'visible',$format); 
+        move("out-$i-Artifact.fastq", "$results_dir/$dest") or die($!);
+    }
+}
+exit;