20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,84 @@
+#!/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 $fastq_dump_path = `sh -c "command -v fastq-dump"`;
+unless ($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;
+}