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comparison roche454/sff_to_fastq_converter.pl @ 0:f036c7107601

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author edward-kirton
date Tue, 07 Jun 2011 17:50:32 -0400
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-1:000000000000 0:f036c7107601
1 #!/usr/bin/env perl
2
3 use warnings;
4 use strict;
5 use Getopt::Long;
6 use File::Basename;
7
8 # VALIDATE INPUT
9 die("Expected 3 args") unless @ARGV == 3;
10 my ($sff, $extra_files_path, $fastq) = @ARGV;
11
12 # DEFINE PATHS
13 mkdir($extra_files_path) unless -d $extra_files_path;
14 my $base = basename($sff);
15 my $fasta = "$extra_files_path/$base.fasta";
16 my $qual = "$extra_files_path/$base.qual";
17
18 # GENERATE FASTA, QUAL, FASTQ
19 my $outf;
20 my $out;
21 eval { $out=`sffinfo -seq $sff > $fasta` };
22 die("ERROR: $out") if $@;
23 print $out;
24 eval { $out=`sffinfo -qual $sff > $qual` };
25 die("ERROR: $out") if $@;
26 print $out;
27 eval { $out=`fasta_qual_to_fastq $fasta $qual $fastq` };
28 die("ERROR: $out") if $@;
29 print $out;
30 unlink($fasta, $qual);
31 exit 0;