roche454_toolsuite: roche454/runMapping_cDNA

annotate roche454/runMapping_cDNA_wrapper.pl @ 1:584549c024c2 default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

author	edward-kirton
date	Tue, 07 Jun 2011 17:23:39 -0400
parents	9e30cc10a6a3
children

rev	line source
0 9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	1 #!/usr/bin/env/perl
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	2
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	3 use warnings;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	4 use strict;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	5 use File::Copy;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	6
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	7 # EXPECT 21 FILE HANDLES, SOME OF WHICH MAY BE 'None'
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	8 my $outdir=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	9 my $alignment_info=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	10 my $all_contigs_fasta=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	11 my $all_contigs_qual=shift @ARGV;
1 584549c024c2 Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository edward-kirton parents: 0 diff changeset	12 my $all_diffs=shift @ARGV;
584549c024c2 Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository edward-kirton parents: 0 diff changeset	13 my $all_struct_vars=shift @ARGV;
584549c024c2 Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository edward-kirton parents: 0 diff changeset	14 my $hc_diff=shift @ARGV;
584549c024c2 Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository edward-kirton parents: 0 diff changeset	15 my $hc_struct_vars=shift @ARGV;
584549c024c2 Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository edward-kirton parents: 0 diff changeset	16 my $mapping_qc=shift @ARGV;
0 9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	17 my $newbler_metrics=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	18 my $pair_align=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	19 my $read_status=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	20 my $ref_status=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	21 my $tag_pair_align=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	22 my $trim_status=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	23 my $trimmed_reads_fasta=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	24 my $trimmed_reads_qual=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	25 my $contigs_ace=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	26 my $gene_status=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	27 my $isotigs_ace=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	28 my $isotigs_fasta=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	29 my $isotigs_qual=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	30 my $isotigs_agp=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	31 my $isotigs_layout=shift @ARGV;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	32
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	33 # REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	34
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	35 my @cmd=removeUnusedOptions(@ARGV);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	36
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	37 # RUN COMMAND
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	38 # NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	39 my $stderr;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	40 eval { $stderr=`@cmd 2>&1`; };
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	41 if ( $@ ) {
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	42 print STDERR "Newbler ERROR: $stderr\n";
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	43 `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	44 die($@);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	45 }
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	46
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	47 get_outfile("$outdir/454AlignmentInfo.tsv", $alignment_info);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	48 get_outfile("$outdir/454AllContigs.fna", $all_contigs_fasta);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	49 get_outfile("$outdir/454AllContigs.qual", $all_contigs_qual);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	50 get_outfile("$outdir/454AllDiffs.txt", $all_diffs);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	51 get_outfile("$outdir/454AllStructVars.txt", $all_struct_vars);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	52 get_outfile("$outdir/454HCDiff.txt", $hc_diff);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	53 get_outfile("$outdir/454HCStructVars.txt", $hc_struct_vars);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	54 get_outfile("$outdir/454MappingQC.xls", $mapping_qc);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	55 get_outfile("$outdir/454NewblerMetrics.txt", $newbler_metrics);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	56 get_outfile("$outdir/454PairAlign.txt", $pair_align);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	57 get_outfile("$outdir/454ReadStatus.txt", $read_status);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	58 get_outfile("$outdir/454RefStatus.txt", $ref_status);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	59 get_outfile("$outdir/454TagPairAlign.txt", $tag_pair_align);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	60 get_outfile("$outdir/454TrimStatus.txt", $trim_status);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	61 get_outfile("$outdir/454TrimmedReads.fna", $trimmed_reads_fasta);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	62 get_outfile("$outdir/454TrimmedReads.qual", $trimmed_reads_qual);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	63 get_outfile("$outdir/454Contigs.ace", $contigs_ace);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	64 get_outfile("$outdir/454GeneStatus.txt", $gene_status);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	65 get_outfile("$outdir/454Isotigs.ace", $isotigs_ace);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	66 get_outfile("$outdir/454Isotigs.fna", $isotigs_fasta);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	67 get_outfile("$outdir/454Isotigs.qual", $isotigs_qual);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	68 get_outfile("$outdir/454Isotigs.txt", $isotigs_agp);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	69 get_outfile("$outdir/454IsotigsLayout.txt", $isotigs_layout);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	70 exit;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	71
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	72 # EVERY 'None' ARG AND IT'S PRECEEDING OPTION TAG ARE DISCARDED
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	73 sub removeUnusedOptions {
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	74 my @cmd=();
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	75 my $prev;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	76 foreach (@_) {
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	77 unless ($_ eq 'None') {
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	78 push @cmd, $prev if defined($prev);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	79 $prev=$_;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	80 } else {
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	81 $prev=undef;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	82 }
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	83 }
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	84 push @cmd, $prev if defined($prev);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	85 return @cmd;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	86 }
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	87
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	88 sub get_outfile {
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	89 my ($src, $dest)=@_;
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	90 # make sure dest defined and src exist; skip if dest is 'None'
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	91 if ( $dest and $dest ne 'None' and $src and -f $src ) {
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	92 move($src,$dest);
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	93 }
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	94 }
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	95
9e30cc10a6a3 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository edward-kirton parents: diff changeset	96 __END__

Mercurial > repos > edward-kirton > roche454_toolsuite

annotate roche454/runMapping_cDNA_wrapper.pl @ 1:584549c024c2 default tip