20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,147 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use Cwd;
+use File::Basename;
+use Carp;
+use Data::Dumper;
+
+use Getopt::Long qw(:config no_ignore_case bundling);
+
+$ENV{LC_ALL} = 'C';  # critical for proper sorting using [system "sort -k1,1 ..."] within the perl script
+
+my $usage = <<_EOUSAGE_;
+
+################################################################################################################
+#
+#  --left and --right <string>   (if paired reads)
+#     or
+#  --single <string>             (if unpaired reads)
+#
+#  Required inputs:
+#   
+#  --target <string>            multi-fasta file containing the target sequences (should be named {refName}.fa )
+#
+#  --out_prefix|o               output prefix (default: bwa)
+#
+# 
+#  ## General options
+#
+#  Any options after '--' are passed onward to the alignments programs (except BLAT -which has certain options exposed above).
+#
+#  To set the number of processors used by BWA use:
+#     -- -t 16
+#  You could also set other options such as 'mismatch penalty' (via -- -M INT), etc. 
+#
+####################################################################################################################
+
+
+
+_EOUSAGE_
+
+    ;
+
+
+my $help_flag;
+my $target_db; 
+my $left_file;
+my $right_file;
+my $single_file;
+
+my $output_prefix = "bwa";
+
+
+unless (@ARGV) {
+    die $usage;
+}
+
+&GetOptions ( 'h' => \$help_flag,
+              
+              ## required inputs
+              'left=s' => \$left_file,
+              'right=s' => \$right_file,
+              
+              'single=s' => \$single_file,
+              
+
+              "target=s" => \$target_db,
+
+              'output_prefix|o=s' => \$output_prefix,
+              
+    );
+
+
+
+
+
+
+if ($help_flag) { die $usage; }
+
+unless ($target_db && -s $target_db) { 
+    die $usage . "Must specify target_db and it must exist at that location";
+}
+
+
+unless ( ($single_file && -e $single_file)
+         || 
+         ($left_file && -e $left_file
+          && $right_file && -e $right_file)) {
+    die $usage . "sorry, cannot find $left_file and $right_file";
+}
+
+####
+sub process_cmd {
+    my ($cmd) = @_;
+
+    print STDERR "CMD: $cmd\n";
+
+    my $ret = system($cmd);
+
+    if ($ret) {
+        confess "Error, cmd: $cmd died with ret $ret";
+    }
+
+    return;
+}
+
+
+
+
+main: {
+
+    
+    my $cmd = "bwa index $target_db";
+    &process_cmd($cmd) unless (-e "$target_db.bwt");;
+    
+    $cmd = "samtools faidx $target_db";
+    &process_cmd($cmd) unless (-e "$target_db.fai");
+    
+
+    if ($left_file && $right_file) {
+
+        $cmd = "bwa aln @ARGV $target_db $left_file > $left_file.sai";
+        &process_cmd($cmd);
+        
+        $cmd = "bwa aln @ARGV $target_db $right_file > $right_file.sai";
+        &process_cmd($cmd);
+        
+        $cmd = "bwa sampe $target_db $left_file.sai $right_file.sai $left_file $right_file | samtools view -bS -F 4 - | samtools sort -o $output_prefix.bam";
+        &process_cmd($cmd);
+        
+    }
+    else {
+                
+        $cmd = "bwa aln @ARGV $target_db $single_file > $single_file.sai";
+        &process_cmd($cmd);
+        
+        $cmd = "bwa samse $target_db $single_file.sai $single_file | samtools view -bS -F 4 - | samtools sort -o $output_prefix.bam";
+        &process_cmd($cmd);
+    }
+    
+    
+    exit(0);
+}
+