Mercurial > repos > edward-kirton > roche454_toolsuite

annotate roche454/runMapping_wrapper.pl @ 0:f036c7107601

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author edward-kirton
date Tue, 07 Jun 2011 17:50:32 -0400
parents
children 368a6ebebdde
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0
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 #!/jgi/tools/bin/perl -w
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2
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3 use strict;
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4 use File::Copy;
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5
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6 # EXPECT 21 FILE HANDLES, SOME OF WHICH MAY BE 'None'
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7 my $outdir=shift @ARGV;
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8 my $alignment_info=shift @ARGV;
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9 my $all_contigs_fasta=shift @ARGV;
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10 my $all_contigs_qual=shift @ARGV;
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11 my $all_diffs=shift @ARGV
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12 my $all_struct_vars=shift @ARGV
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13 my $hc_diff=shift @ARGV
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14 my $hc_struct_vars=shift @ARGV
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15 my $mapping_qc=shift @ARGV
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16 my $newbler_metrics=shift @ARGV;
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17 my $pair_align=shift @ARGV;
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18 my $read_status=shift @ARGV;
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19 my $ref_status=shift @ARGV;
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20 my $tag_pair_align=shift @ARGV;
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21 my $trim_status=shift @ARGV;
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22 my $trimmed_reads_fasta=shift @ARGV;
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23 my $trimmed_reads_qual=shift @ARGV;
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24 my $contigs_ace=shift @ARGV;
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25 my $large_contigs_fasta=shift @ARGV;
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26 my $large_contigs_qual=shift @ARGV;
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27 my $gene_status=shift @ARGV;
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28
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29 # REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED
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30
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31 my @cmd=removeUnusedOptions(@ARGV);
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32
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33 # RUN COMMAND
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34 # NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
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35 my $stderr;
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36 eval { $stderr=`@cmd 2>&1`; };
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37 if ( $@ ) {
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38 print STDERR "Newbler ERROR: $stderr\n";
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39 `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
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40 die($@);
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41 }
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42
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43 get_outfile("$outdir/454AlignmentInfo.tsv", $alignment_info);
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44 get_outfile("$outdir/454AllContigs.fna", $all_contigs_fasta);
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45 get_outfile("$outdir/454AllContigs.qual", $all_contigs_qual);
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46 get_outfile("$outdir/454AllDiffs.txt", $all_diffs);
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47 get_outfile("$outdir/454AllStructVars.txt", $all_struct_vars);
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48 get_outfile("$outdir/454HCDiff.txt", $hc_diff);
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49 get_outfile("$outdir/454HCStructVars.txt", $hc_struct_vars);
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50 get_outfile("$outdir/454MappingQC.xls", $mapping_qc);
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51 get_outfile("$outdir/454NewblerMetrics.txt", $newbler_metrics);
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52 get_outfile("$outdir/454PairAlign.txt", $pair_align);
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53 get_outfile("$outdir/454ReadStatus.txt", $read_status);
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54 get_outfile("$outdir/454RefStatus.txt", $ref_status);
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55 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
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56 get_outfile("$outdir/454TrimStatus.txt", $trim_status);
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57 get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
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58 get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
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59 get_outfile("$outdir/454Contigs.ace", $contigs_ace);
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60 get_outfile("$outdir/454LargeContigs.fna", $large_contigs_fasta);
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61 get_outfile("$outdir/454LargeContigs.qual", $large_contigs_qual);
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62 get_outfile("$outdir/454GeneStatus.txt", $gene_status);
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63 exit;
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64
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65 # EVERY 'None' ARG AND IT'S PRECEEDING OPTION TAG ARE DISCARDED
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66 sub removeUnusedOptions {
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67 my @cmd=();
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68 my $prev;
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69 foreach (@_) {
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70 unless ($_ eq 'None') {
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71 push @cmd, $prev if defined($prev);
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72 $prev=$_;
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73 } else {
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74 $prev=undef;
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75 }
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76 }
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77 push @cmd, $prev if defined($prev);
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78 return @cmd;
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79 }
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80
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81 sub get_outfile {
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82 my ($src, $dest)=@_;
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83 # make sure dest defined and src exist; skip if dest is 'None'
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84 if ( $dest and $dest ne 'None' and $src and -f $src ) {
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85 move($src,$dest);
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86 }
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87 }
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88
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89 __END__