54 lines
1.9 KiB
Perl
Executable File
54 lines
1.9 KiB
Perl
Executable File
#!/usr/bin/perl -w
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# Runs the TranscriptToGenomicInfo tool to create big tables
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use strict;
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use Getopt::Long;
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my $in = undef;
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my $gatk = undef;
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my $ref = undef;
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my $out = undef;
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my $tmp = "/tmp";
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GetOptions( "transcript=s" => \$in,
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"gatk=s" => \$gatk,
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"ref=s" => \$ref,
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"out=s" => \$out,
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"tmp=s" => \$tmp);
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if ( !$in || !$gatk || !$ref || !$out ) {
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print "Usage: createTranscriptToGenomicInfoTables.pl\n\t-transcript \t<raw transcript input table>\n\t-gatk \t\t<path to gatk trunk>\n\t-ref \t\t<path to reference.fasta>\n\t-out \t\t<genomic output table>\n\t-tmp \t\t<temp file location; needs potentially lots of space; defaults to /tmp>\n";
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print "Example: ./createTranscriptToGenomicInfoTables.pl\n\t-transcript test.foo\n\t-ref /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta\n\t-gatk /humgen/gsa-scr1/ebanks/Sting_dev\n\t-out test.bar\n\t-tmp /broad/shptmp\n";
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exit(1);
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}
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# generate a random number
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my $random_number = rand();
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my $tmp_prefix = "$tmp/$random_number";
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print "Writing temporary files to prefix: $tmp_prefix\n";
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my $unsorted_table = "$tmp_prefix.unsorted.table";
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# convert the file
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print "Converting the transcript table...";
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my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T TranscriptToGenomicInfo -R $ref -B:transcripts,AnnotatorInputTable $in -o $unsorted_table -n name,proteinID";
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system($cmd);
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# we need to sort the converted table now
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print "\nRe-sorting the table...\n";
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open(SORTED, ">$out") or die "can't open $out: $!";
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# write the header
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open(UNSORTED, "< $unsorted_table") or die "can't open $unsorted_table: $!";
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my $line = <UNSORTED>;
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print SORTED "$line";
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close(UNSORTED);
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$cmd = "grep haplotypeReference -v $unsorted_table | sort -n -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $ref.fai";
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print SORTED `$cmd`;
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close(SORTED);
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# clean up
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unlink $unsorted_table;
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print "\nDone!\n";
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