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