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2
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1 #!/usr/bin/env/perl
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2
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3 use warnings;
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4 use strict;
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5 use File::Copy;
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6
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7 # EXPECT 24 FILE HANDLES, SOME OF WHICH MAY BE 'None'
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8 die("Missing arguments; expected at least 24, got ".scalar(@ARGV)."\n") unless @ARGV >= 24;
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9 my $outdir=shift @ARGV;
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10 my $alignment_info=shift @ARGV;
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11 my $all_contigs_fasta=shift @ARGV;
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12 my $all_contigs_qual=shift @ARGV;
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13 my $all_diffs=shift @ARGV;
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14 my $all_struct_vars=shift @ARGV;
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15 my $hc_diff=shift @ARGV;
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16 my $hc_struct_vars=shift @ARGV;
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17 my $mapping_qc=shift @ARGV;
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18 my $newbler_metrics=shift @ARGV;
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19 my $pair_align=shift @ARGV;
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20 my $read_status=shift @ARGV;
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21 my $ref_status=shift @ARGV;
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22 my $tag_pair_align=shift @ARGV;
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23 my $trim_status=shift @ARGV;
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24 my $trimmed_reads_fasta=shift @ARGV;
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25 my $trimmed_reads_qual=shift @ARGV;
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26 my $contigs_ace=shift @ARGV;
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27 my $gene_status=shift @ARGV;
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28 my $isotigs_ace=shift @ARGV;
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29 my $isotigs_fasta=shift @ARGV;
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30 my $isotigs_qual=shift @ARGV;
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31 my $isotigs_agp=shift @ARGV;
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32 my $isotigs_layout=shift @ARGV;
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33
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34 # REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED
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35
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36 my @cmd=removeUnusedOptions(@ARGV);
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37
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38 # RUN COMMAND
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39 my $stderr;
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3
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40 eval { $stderr=`runMapping @cmd 2>&1`; };
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2
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41 if ( $@ ) {
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42 print STDERR "Newbler ERROR: $stderr\n";
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43 `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
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44 die($@);
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45 }
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46
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47 get_outfile("$outdir/454AlignmentInfo.tsv", $alignment_info);
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48 get_outfile("$outdir/454AllContigs.fna", $all_contigs_fasta);
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49 get_outfile("$outdir/454AllContigs.qual", $all_contigs_qual);
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50 get_outfile("$outdir/454AllDiffs.txt", $all_diffs);
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51 get_outfile("$outdir/454AllStructVars.txt", $all_struct_vars);
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52 get_outfile("$outdir/454HCDiff.txt", $hc_diff);
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53 get_outfile("$outdir/454HCStructVars.txt", $hc_struct_vars);
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54 get_outfile("$outdir/454MappingQC.xls", $mapping_qc);
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55 get_outfile("$outdir/454NewblerMetrics.txt", $newbler_metrics);
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56 get_outfile("$outdir/454PairAlign.txt", $pair_align);
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57 get_outfile("$outdir/454ReadStatus.txt", $read_status);
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58 get_outfile("$outdir/454RefStatus.txt", $ref_status);
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59 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
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60 get_outfile("$outdir/454TrimStatus.txt", $trim_status);
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61 get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
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62 get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
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63 get_outfile("$outdir/454Contigs.ace", $contigs_ace);
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64 get_outfile("$outdir/454GeneStatus.txt", $gene_status);
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65 get_outfile("$outdir/454Isotigs.ace", $isotigs_ace);
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66 get_outfile("$outdir/454Isotigs.fna", $isotigs_fasta);
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67 get_outfile("$outdir/454Isotigs.qual", $isotigs_qual);
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68 get_outfile("$outdir/454Isotigs.txt", $isotigs_agp);
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69 get_outfile("$outdir/454IsotigsLayout.txt", $isotigs_layout);
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70 exit;
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71
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72 # EVERY 'None' ARG AND IT'S PRECEEDING OPTION TAG ARE DISCARDED
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73 sub removeUnusedOptions {
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74 my @cmd=();
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75 my $prev;
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76 foreach (@_) {
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77 unless ($_ eq 'None') {
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78 push @cmd, $prev if defined($prev);
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79 $prev=$_;
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80 } else {
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81 $prev=undef;
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82 }
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83 }
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84 push @cmd, $prev if defined($prev);
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85 return @cmd;
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86 }
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87
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88 sub get_outfile {
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89 my ($src, $dest)=@_;
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90 # make sure dest defined and src exist; skip if dest is 'None'
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91 if ( $dest and $dest ne 'None' and $src and -f $src ) {
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92 move($src,$dest);
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93 }
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94 }
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95
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96 __END__
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