Mercurial > repos > edward-kirton > roche454_toolsuite
comparison runMapping_wrapper.pl @ 3:bf1f8bc4abe6 default tip
minor updates for v2.6
author | eskirton@lbl.gov |
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date | Wed, 21 Dec 2011 19:42:53 -0800 |
parents | 2d86d5b112e8 |
children |
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2:2d86d5b112e8 | 3:bf1f8bc4abe6 |
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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 |