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