20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,53 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+
+my $usage = "usage: $0 Trinity.fasta reads.{fa,fq}\n\n";
+
+my $trinity_fasta = $ARGV[0] or die $usage;
+my $reads_fasta = $ARGV[1] or die $usage;
+
+
+main: {
+
+    my $cmd = "fasta_file_header_stripper.pl < $trinity_fasta > $trinity_fasta.noheader";
+    &process_cmd($cmd);
+
+    $cmd = "bwa index -a is $trinity_fasta.noheader";
+    &process_cmd($cmd);
+
+    $cmd = "samtools faidx $trinity_fasta.noheader";
+    &process_cmd($cmd);
+
+    my $outfile_prefix = basename($reads_fasta);
+    $cmd = "bwa bwasw $trinity_fasta.noheader $reads_fasta > $outfile_prefix.sam";
+    &process_cmd($cmd);
+
+    $cmd = "samtools view -bt $trinity_fasta.noheader.fai $outfile_prefix.sam > $outfile_prefix.bam";
+    &process_cmd($cmd);
+
+    $cmd = "samtools sort $outfile_prefix.bam -o $outfile_prefix.bam ";
+    &process_cmd($cmd);
+
+    $cmd = "samtools index $outfile_prefix.bam";
+    &process_cmd($cmd);
+
+    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;
+}