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#!/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;
}
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