Mercurial > repos > edward-kirton > roche454_toolsuite

comparison runAssembly_cDNA_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
20 my $pair_align=shift @ARGV; 20 my $pair_align=shift @ARGV;
21 my $pair_status=shift @ARGV; 21 my $pair_status=shift @ARGV;
22 my $scaffolds_fasta=shift @ARGV; 22 my $scaffolds_fasta=shift @ARGV;
23 my $scaffolds_qual=shift @ARGV; 23 my $scaffolds_qual=shift @ARGV;
24 my $scaffolds_agp=shift @ARGV; 24 my $scaffolds_agp=shift @ARGV;
25 my $contig_scaffolds_agp=shift @ARGV;
25 my $tag_pair_align=shift @ARGV; 26 my $tag_pair_align=shift @ARGV;
26 my $trim_status=shift @ARGV; 27 my $trim_status=shift @ARGV;
27 my $isotigs_ace=shift @ARGV; 28 my $isotigs_ace=shift @ARGV;
28 my $isotigs_fasta=shift @ARGV; 29 my $isotigs_fasta=shift @ARGV;
29 my $isotigs_qual=shift @ARGV; 30 my $isotigs_qual=shift @ARGV;
33 # REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED 34 # REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED
34 35
35 my @cmd=removeUnusedOptions(@ARGV); 36 my @cmd=removeUnusedOptions(@ARGV);
36 37
37 # RUN COMMAND 38 # RUN COMMAND
38 # NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
39 my $stderr; 39 my $stderr;
40 eval { $stderr=`@cmd 2>&1`; }; 40 eval { $stderr=`runAssembly @cmd 2>&1`; };
41 if ( $@ ) { 41 if ( $@ ) {
42 print STDERR "Newbler ERROR: $stderr\n"; 42 print STDERR "Newbler ERROR: $stderr\n";
43 `cat $outdir/assembly/454NewblerProgress.txt 1>&2`; 43 `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
44 die($@); 44 die($@);
45 } 45 }
57 get_outfile("$outdir/454PairAlign.txt", $pair_align); 57 get_outfile("$outdir/454PairAlign.txt", $pair_align);
58 get_outfile("$outdir/454PairStatus.txt", $pair_status); 58 get_outfile("$outdir/454PairStatus.txt", $pair_status);
59 get_outfile("$outdir/454Scaffolds.fna", $scaffolds_fasta); 59 get_outfile("$outdir/454Scaffolds.fna", $scaffolds_fasta);
60 get_outfile("$outdir/454Scaffolds.qual", $scaffolds_qual); 60 get_outfile("$outdir/454Scaffolds.qual", $scaffolds_qual);
61 get_outfile("$outdir/454Scaffolds.txt", $scaffolds_agp); 61 get_outfile("$outdir/454Scaffolds.txt", $scaffolds_agp);
62 get_outfile("$outdir/454ContigScaffolds.txt", $contig_scaffolds_agp);
62 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align); 63 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
63 get_outfile("$outdir/454TrimStatus.txt", $trim_status); 64 get_outfile("$outdir/454TrimStatus.txt", $trim_status);
64 get_outfile("$outdir/454Isotigs.ace", $isotigs_ace); 65 get_outfile("$outdir/454Isotigs.ace", $isotigs_ace);
65 get_outfile("$outdir/454Isotigs.fna", $isotigs_fasta); 66 get_outfile("$outdir/454Isotigs.fna", $isotigs_fasta);
66 get_outfile("$outdir/454Isotigs.qual", $isotigs_qual); 67 get_outfile("$outdir/454Isotigs.qual", $isotigs_qual);