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comparison snippy_core_wrapper.pl @ 6:15f5a3074012 draft

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Added snippy core and static binaries for linux and mac.
author simon-gladman
date Thu, 09 Jun 2016 20:15:42 -0400
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5:ff31f16f5dfd 6:15f5a3074012
1 #!/usr/bin/env perl
2
3 #--------------------------------------
4 #
5 # snippy_core_wrapper.pl
6 #
7 # This is an intermediary script between snippy-core.xml and snippy-core
8 # It:
9 # - Copys the supplied zipped snippy output files to the working dir
10 # - Untars them to their datafile name
11 # - Builds the snippy-core command and captures the stdout and stderr to files
12 # - Runs the snippy-core command
13 #
14 #--------------------------------------
15
16 use warnings;
17 use strict;
18 use File::Copy;
19 use File::Basename;
20
21 my(@Options, $indirs, $mincov, $noref);
22 setOptions();
23
24 my @list_of_dirs = split /\s+/, $indirs;
25
26 #The list of final directories to be passed to snippy-core will be stored here.
27 my @snippy_outs;
28
29 foreach my $d (@list_of_dirs){
30 #print STDERR "$d\n";
31 my $bn = basename($d);
32 my ($name, $dir, $ext) = fileparse($d, '\..*');
33 copy($d, $bn);
34 #print STDERR "$d, $bn, $name, $dir, $ext\n";
35 `tar -xf $bn`;
36 move("./out", "./$name");
37 unlink($bn);
38 push @snippy_outs, $name;
39 }
40
41 my $commandline = "snippy-core ";
42
43 $commandline .= "--noref " if $noref;
44 $commandline .= "--mincov $mincov " if $mincov;
45 $commandline .= join(" ", @snippy_outs);
46 print STDERR "snippy-core commandline: $commandline\n";
47
48 my $ok = system($commandline);
49
50 #----------------------------------------------------------------------
51 # Option setting routines
52
53 sub setOptions {
54 use Getopt::Long;
55
56 @Options = (
57 {OPT=>"help", VAR=>\&usage, DESC=>"This help"},
58 {OPT=>"mincov=i", VAR=>\$mincov, DEFAULT=>'10.0', DESC=>"The minimum coverage to consider."},
59 {OPT=>"noref!", VAR=>\$noref, DEFAULT=>0, DESC=>"Don't include the reference in the alignment."},
60 {OPT=>"indirs=s", VAR=>\$indirs, DEFAULT=>"", DESC=>"A whitespace delimited list of the snippy output zipped dirs."},
61 );
62
63 &GetOptions(map {$_->{OPT}, $_->{VAR}} @Options) || usage();
64
65 # Now setup default values.
66 foreach (@Options) {
67 if (defined($_->{DEFAULT}) && !defined(${$_->{VAR}})) {
68 ${$_->{VAR}} = $_->{DEFAULT};
69 }
70 }
71 }
72
73 sub usage {
74 print "Usage: $0 [options] -i inputfile > ... \n";
75 foreach (@Options) {
76 printf " --%-13s %s%s.\n",$_->{OPT},$_->{DESC},
77 defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
78 }
79 exit(1);
80 }