Mercurial > repos > edward-kirton > roche454_toolsuite

comparison runMapping_wrapper.pl @ 3:bf1f8bc4abe6 default tip

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minor updates for v2.6
author eskirton@lbl.gov
date Wed, 21 Dec 2011 19:42:53 -0800
parents 2d86d5b112e8
children
comparison
equal deleted inserted replaced
2:2d86d5b112e8 3:bf1f8bc4abe6
21 my $tag_pair_align=shift @ARGV; 21 my $tag_pair_align=shift @ARGV;
22 my $trim_status=shift @ARGV; 22 my $trim_status=shift @ARGV;
23 my $trimmed_reads_fasta=shift @ARGV; 23 my $trimmed_reads_fasta=shift @ARGV;
24 my $trimmed_reads_qual=shift @ARGV; 24 my $trimmed_reads_qual=shift @ARGV;
25 my $contigs_ace=shift @ARGV; 25 my $contigs_ace=shift @ARGV;
26 my $contigs_bam=shift @ARGV;
26 my $large_contigs_fasta=shift @ARGV; 27 my $large_contigs_fasta=shift @ARGV;
27 my $large_contigs_qual=shift @ARGV; 28 my $large_contigs_qual=shift @ARGV;
28 my $gene_status=shift @ARGV; 29 my $gene_status=shift @ARGV;
29 30
30 # REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED 31 # REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED
31 32
32 my @cmd=removeUnusedOptions(@ARGV); 33 my @cmd=removeUnusedOptions(@ARGV);
33 34
34 # RUN COMMAND 35 # RUN COMMAND
35 # NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
36 my $stderr; 36 my $stderr;
37 eval { $stderr=`@cmd 2>&1`; }; 37 eval { $stderr=`runMapping @cmd 2>&1`; };
38 if ( $@ ) { 38 if ( $@ ) {
39 print STDERR "Newbler ERROR: $stderr\n"; 39 print STDERR "Newbler ERROR: $stderr\n";
40 `cat $outdir/assembly/454NewblerProgress.txt 1>&2`; 40 `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
41 die($@); 41 die($@);
42 } 42 }
56 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align); 56 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
57 get_outfile("$outdir/454TrimStatus.txt", $trim_status); 57 get_outfile("$outdir/454TrimStatus.txt", $trim_status);
58 get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta); 58 get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
59 get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual); 59 get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
60 get_outfile("$outdir/454Contigs.ace", $contigs_ace); 60 get_outfile("$outdir/454Contigs.ace", $contigs_ace);
61 get_outfile("$outdir/454Contigs.bam", $contigs_bam);
61 get_outfile("$outdir/454LargeContigs.fna", $large_contigs_fasta); 62 get_outfile("$outdir/454LargeContigs.fna", $large_contigs_fasta);
62 get_outfile("$outdir/454LargeContigs.qual", $large_contigs_qual); 63 get_outfile("$outdir/454LargeContigs.qual", $large_contigs_qual);
63 get_outfile("$outdir/454GeneStatus.txt", $gene_status); 64 get_outfile("$outdir/454GeneStatus.txt", $gene_status);
64 exit; 65 exit;
65 66