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#!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = "\n\nusage: $0 --prefix \$prefix fileA.sra [fileB.sra ...]\n\n\n";
my $prefix;
&GetOptions ('prefix=s' => \$prefix);
my @sra_files = @ARGV;
unless (@ARGV) {
die $usage;
}
unless (@sra_files) {
die $usage;
}
my $fastq_dump_path = `which fastq-dump`;
unless ($fastq_dump_path && $fastq_dump_path =~ /\w/) {
die "Error, cannot find 'fastq-dump' utility in your PATH. Be sure you have SRA toolkit installed and fastq-dump in your PATH setting. ";
}
my @core_names;
foreach my $sra_file (@sra_files) {
my $core_name = $sra_file;
$core_name =~ s/\.sra$//;
$core_name = basename($core_name);
push (@core_names, $core_name);
my $cmd = "fastq-dump --defline-seq '@\$sn[_\$rn]/\$ri' --split-files $sra_file";
&process_cmd($cmd) unless (-s "${core_name}_1.fastq");
}
if ($prefix) {
my @final_cmds;
my @tmp_files;
for my $end ("1", "2") {
my $cmd = "cat";
foreach my $core_name (@core_names) {
my $file = "$core_name" . "_$end.fastq";
$cmd .= " $file ";
push (@tmp_files, $file);
}
$cmd .= ">$prefix" . "_$end.fastq";
&process_cmd($cmd);
}
## remove tmp files:
foreach my $file (@tmp_files) {
unlink($file);
}
}
exit(0);
####
sub process_cmd {
my ($cmd) = @_;
print STDERR "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
return;
}
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