53 lines
1.2 KiB
Perl
53 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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my $usage = "usage: $0 genome.fasta left.fq right.fq [output_dir]\n\n";
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my $genome_file = $ARGV[0] or die $usage;
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my $left_fq_file = $ARGV[1] or die $usage;
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my $right_fq_file = $ARGV[2] or die $usage;
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my $output_dir = $ARGV[3] || "bowtie.$$.dir";
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while ($output_dir =~ m|/$|) {
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chop $output_dir;
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}
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main: {
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## run bowtie
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my $cmd = "$FindBin::RealBin/../alignReads.pl --target $genome_file --left $left_fq_file --right $right_fq_file "
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. " --seqType fq --aligner bowtie -o $output_dir --max_dist_between_pairs 900000000 --no_rsem --retain_intermediate_files "
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. " -- -a -m 1 --best --strata -p 4 --chunkmbs 512 ";
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&process_cmd($cmd) unless (-s "$output_dir/$output_dir.nameSorted.sam");
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$cmd = "$FindBin::RealBin/HiCpipe_nameSortedSam_to_raw.pl $output_dir/$output_dir.nameSorted.sam > $output_dir/$output_dir.raw";
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&process_cmd($cmd) unless (-s "$output_dir/$output_dir.raw");
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exit(0);
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}
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####
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sub process_cmd {
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my ($cmd) = @_;
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print STDERR "CMD: $cmd\n";
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my $ret = system($cmd);
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if ($ret) {
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die "Error, cmd: $cmd died with ret $ret";
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}
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return;
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}
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