Mercurial > repos > edward-kirton > roche454_toolsuite
view roche454/sff_to_fastq_converter.pl @ 1:368a6ebebdde
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | edward-kirton |
---|---|
date | Tue, 07 Jun 2011 17:51:04 -0400 |
parents | f036c7107601 |
children |
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#!/usr/bin/env perl use warnings; use strict; use Getopt::Long; use File::Basename; # VALIDATE INPUT die("Expected 3 args") unless @ARGV == 3; my ($sff, $extra_files_path, $fastq) = @ARGV; # DEFINE PATHS mkdir($extra_files_path) unless -d $extra_files_path; my $base = basename($sff); my $fasta = "$extra_files_path/$base.fasta"; my $qual = "$extra_files_path/$base.qual"; # GENERATE FASTA, QUAL, FASTQ my $outf; my $out; eval { $out=`sffinfo -seq $sff > $fasta` }; die("ERROR: $out") if $@; print $out; eval { $out=`sffinfo -qual $sff > $qual` }; die("ERROR: $out") if $@; print $out; eval { $out=`fasta_qual_to_fastq $fasta $qual $fastq` }; die("ERROR: $out") if $@; print $out; unlink($fasta, $qual); exit 0;