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Revision 1.1 - (view) (download) (as text)
| 1 : | arodri7 | 1.1 | |
| 2 : | # | ||
| 3 : | # dereplication of the input fasta. | ||
| 4 : | # | ||
| 5 : | |||
| 6 : | use strict; | ||
| 7 : | use FIG; | ||
| 8 : | use FIG_Config; | ||
| 9 : | use File::Basename; | ||
| 10 : | use GenomeMeta; | ||
| 11 : | use Job48; | ||
| 12 : | use JobStage; | ||
| 13 : | use SGE; | ||
| 14 : | use FortyEightMeta::SimDB; | ||
| 15 : | use FortyEightMeta::SimStatusDB; | ||
| 16 : | |||
| 17 : | my $STAGE = "dereplication"; | ||
| 18 : | |||
| 19 : | @ARGV == 1 or die "Usage: $0 job-dir\n"; | ||
| 20 : | |||
| 21 : | my $jobdir = shift; | ||
| 22 : | |||
| 23 : | -d $jobdir or die "$0: job dir $jobdir does not exist\n"; | ||
| 24 : | |||
| 25 : | my $stage = new JobStage('Job48', $STAGE, $jobdir); | ||
| 26 : | $stage or die "Cannot create job for $jobdir\n"; | ||
| 27 : | |||
| 28 : | my $job_id = basename($jobdir); | ||
| 29 : | my $job = $stage->job(); | ||
| 30 : | |||
| 31 : | my $meta = $job->meta; | ||
| 32 : | |||
| 33 : | print "Running job! $jobdir\n"; | ||
| 34 : | |||
| 35 : | $stage->set_status("in_progress"); | ||
| 36 : | |||
| 37 : | # | ||
| 38 : | # Find needed executables | ||
| 39 : | # | ||
| 40 : | |||
| 41 : | #my $dereplication_exe = "/home/arodri7/public_html/FIGdisk/dist/releases/dev/MGRASTBackend/scripts/sequence_dereplication.pl"; | ||
| 42 : | my $dereplication_exe = "$FIG_Config::bin/sequence_dereplication"; | ||
| 43 : | -x $dereplication_exe or $stage->fatal("Executable missing: $dereplication_exe"); | ||
| 44 : | |||
| 45 : | my $proc = "$jobdir/proc"; | ||
| 46 : | chdir($proc) or $stage->fatal("cannot chdir $proc: $!"); | ||
| 47 : | |||
| 48 : | my $fasta = $meta->get_metadata("preprocess.fasta_file"); | ||
| 49 : | ($fasta and -f $fasta) or $stage->fatal("fasta not found: '$fasta'"); | ||
| 50 : | |||
| 51 : | my $new_fasta = "dereplication.fasta"; | ||
| 52 : | |||
| 53 : | |||
| 54 : | $stage->log("Dereplication original=$fasta new_fasta=$new_fasta"); | ||
| 55 : | |||
| 56 : | my $stderr = "$jobdir/errors/$STAGE.stderr"; | ||
| 57 : | my $cmd = "$dereplication_exe -f $fasta -o $new_fasta -v"; | ||
| 58 : | open(P, "$cmd |") or $stage->fatal("Failed pipe open: $!: $cmd"); | ||
| 59 : | open(E, ">$stderr") or $stage->fata("Failed stderr open $!: $stderr"); | ||
| 60 : | my($start, $end); | ||
| 61 : | while (<P>) | ||
| 62 : | { | ||
| 63 : | print E $_; | ||
| 64 : | } | ||
| 65 : | close(P) or $stage->fatal("Error on close: \$!=$! \$?=$?: $cmd"); | ||
| 66 : | close(E); | ||
| 67 : | |||
| 68 : | $stage->set_qualified_metadata("fasta_file", $new_fasta); | ||
| 69 : | $stage->set_status("complete"); | ||
| 70 : | $stage->set_running("no"); | ||
| 71 : | |||
| 72 : | |||
| 73 : |
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