Mercurial > repos > simon-gladman > snippy

annotate snippy_core_wrapper.pl @ 7:93d294cd4d59 draft default tip

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Added snippy core
author simon-gladman
date Fri, 10 Jun 2016 00:10:22 -0400
parents 15f5a3074012
children
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6
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1 #!/usr/bin/env perl
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2
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3 #--------------------------------------
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4 #
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5 # snippy_core_wrapper.pl
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6 #
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7 # This is an intermediary script between snippy-core.xml and snippy-core
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8 # It:
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9 # - Copys the supplied zipped snippy output files to the working dir
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10 # - Untars them to their datafile name
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11 # - Builds the snippy-core command and captures the stdout and stderr to files
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12 # - Runs the snippy-core command
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13 #
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14 #--------------------------------------
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15
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16 use warnings;
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17 use strict;
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18 use File::Copy;
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19 use File::Basename;
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20
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21 my(@Options, $indirs, $mincov, $noref);
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22 setOptions();
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23
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24 my @list_of_dirs = split /\s+/, $indirs;
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25
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26 #The list of final directories to be passed to snippy-core will be stored here.
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27 my @snippy_outs;
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28
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29 foreach my $d (@list_of_dirs){
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30 #print STDERR "$d\n";
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31 my $bn = basename($d);
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32 my ($name, $dir, $ext) = fileparse($d, '\..*');
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33 copy($d, $bn);
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34 #print STDERR "$d, $bn, $name, $dir, $ext\n";
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35 `tar -xf $bn`;
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36 move("./out", "./$name");
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37 unlink($bn);
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38 push @snippy_outs, $name;
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39 }
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40
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41 my $commandline = "snippy-core ";
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42
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43 $commandline .= "--noref " if $noref;
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44 $commandline .= "--mincov $mincov " if $mincov;
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45 $commandline .= join(" ", @snippy_outs);
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46 print STDERR "snippy-core commandline: $commandline\n";
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47
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48 my $ok = system($commandline);
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49
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50 #----------------------------------------------------------------------
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51 # Option setting routines
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52
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53 sub setOptions {
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54 use Getopt::Long;
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55
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56 @Options = (
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57 {OPT=>"help", VAR=>\&usage, DESC=>"This help"},
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58 {OPT=>"mincov=i", VAR=>\$mincov, DEFAULT=>'10.0', DESC=>"The minimum coverage to consider."},
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59 {OPT=>"noref!", VAR=>\$noref, DEFAULT=>0, DESC=>"Don't include the reference in the alignment."},
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60 {OPT=>"indirs=s", VAR=>\$indirs, DEFAULT=>"", DESC=>"A whitespace delimited list of the snippy output zipped dirs."},
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61 );
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62
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63 &GetOptions(map {$_->{OPT}, $_->{VAR}} @Options) || usage();
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64
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65 # Now setup default values.
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66 foreach (@Options) {
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67 if (defined($_->{DEFAULT}) && !defined(${$_->{VAR}})) {
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68 ${$_->{VAR}} = $_->{DEFAULT};
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69 }
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70 }
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71 }
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72
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73 sub usage {
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74 print "Usage: $0 [options] -i inputfile > ... \n";
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75 foreach (@Options) {
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76 printf " --%-13s %s%s.\n",$_->{OPT},$_->{DESC},
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77 defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
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78 }
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79 exit(1);
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80 }