20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,50 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib("$FindBin::Bin/../../PerlLib");
+use Pipeliner;
+use Cwd;
+
+
+my $usage = "\n\n\tusage: $0 input.fasta reads.left.[fq|fa] reads.right.[fq|fa]\n\n";
+
+my $target_fa = $ARGV[0] or die $usage;
+my $left_reads = $ARGV[1] or die $usage;
+my $right_reads = $ARGV[2] or die $usage;
+
+unless ($target_fa =~ /^\//) {
+    $target_fa = cwd() . "/$target_fa";
+}
+
+main: {
+
+    my $pipeliner = new Pipeliner('-verbose' => 2);
+
+    $pipeliner->add_commands(new Command("samtools faidx $target_fa", "$target_fa.fai.ok"));
+    
+    my $cmd = "bowtie2-build $target_fa $target_fa";
+    $pipeliner->add_commands(new Command($cmd, "$target_fa.bowtie2-build.ok"));
+
+
+    my $format = ($left_reads =~ /q$/i) ? '-q' : '-f';
+
+    my $alignments_file = cwd() . "/alignments.$$.bam";
+    
+    $cmd = "set -eof pipefail; bowtie2 --no-unal -X 1000 -x $target_fa $format -1 $left_reads -2 $right_reads | samtools view -Sb - | samtools sort  > $alignments_file";
+    $pipeliner->add_commands(new Command($cmd, "$alignments_file.ok"));
+
+    $pipeliner->add_commands(new Command("samtools index $alignments_file", "$alignments_file.bai.ok"));
+
+    $pipeliner->run();
+
+    system("igv.sh -g $target_fa $alignments_file");
+
+
+    exit(0);
+}
+
+
+