49 lines
1.1 KiB
Perl
49 lines
1.1 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 Process_cmd;
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my $usage = "\n\n\tusage: $0 Trinity.fasta reads.fa [threads=1]\n\n";
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my $trin_fa = $ARGV[0] or die $usage;
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my $reads_fa = $ARGV[1] or die $usage;
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my $CPU = $ARGV[2] || 1;
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main: {
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my $salmon_index = "$trin_fa.salmon.idx";
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my $salmon_stderr = "_salmon.$$.stderr";
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my $cmd = "salmon --no-version-check index -t $trin_fa -i $salmon_index -k 25 -p $CPU > $salmon_stderr 2>&1";
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&run_cmd_capture_stderr($cmd, $salmon_stderr);
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$cmd = "salmon --no-version-check quant -i $salmon_index -l U -r $reads_fa -o salmon_outdir -p $CPU --minAssignedFrags 1 --validateMappings > $salmon_stderr 2>&1";
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&run_cmd_capture_stderr($cmd, $salmon_stderr);
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unlink($salmon_stderr);
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exit(0);
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}
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####
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sub run_cmd_capture_stderr {
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my ($cmd, $stderr_file) = @_;
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eval {
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&process_cmd($cmd);
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};
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if ($@) {
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my $errmsg = `cat $stderr_file`;
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die "Error, cmd: $cmd failed with msg: $errmsg $@";
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}
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return;
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}
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