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view snippy_core_wrapper.pl @ 0:c9a8ef2aa380 draft
planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7
author | iuc |
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date | Fri, 16 Feb 2018 13:40:16 -0500 |
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#!/usr/bin/env perl #-------------------------------------- # # snippy_core_wrapper.pl # # This is an intermediary script between snippy-core.xml and snippy-core # It: # - Copys the supplied zipped snippy output files to the working dir # - Untars them to their datafile name # - Builds the snippy-core command # - Runs the snippy-core command # #-------------------------------------- use warnings; use strict; use File::Copy; use File::Basename; my(@Options, $indirs, $noref); setOptions(); my @list_of_dirs = split /\s+/, $indirs; #The list of final directories to be passed to snippy-core will be stored here. my @snippy_outs; foreach my $d (@list_of_dirs){ print STDERR "$d\n"; my $bn = basename($d); my ($name, $dir, $ext) = fileparse($d, '\..*'); copy($d, $bn); print STDERR "$d, $bn, $name, $dir, $ext\n"; `tar -xf $bn`; } my $test_list = `ls -d */`; $test_list =~ s/\///g; print STDERR "$test_list\n"; @snippy_outs = split /\s+/, $test_list; my $commandline = "snippy-core "; $commandline .= "--noref " if $noref; $commandline .= join(" ", @snippy_outs); print STDERR "snippy-core commandline: $commandline\n"; my $ok = system($commandline); #---------------------------------------------------------------------- # Option setting routines sub setOptions { use Getopt::Long; @Options = ( {OPT=>"help", VAR=>\&usage, DESC=>"This help"}, {OPT=>"noref!", VAR=>\$noref, DEFAULT=>0, DESC=>"Don't include the reference in the alignment."}, {OPT=>"indirs=s", VAR=>\$indirs, DEFAULT=>"", DESC=>"A whitespace delimited list of the snippy output zipped dirs."}, ); &GetOptions(map {$_->{OPT}, $_->{VAR}} @Options) || usage(); # Now setup default values. foreach (@Options) { if (defined($_->{DEFAULT}) && !defined(${$_->{VAR}})) { ${$_->{VAR}} = $_->{DEFAULT}; } } } sub usage { print "Usage: $0 [options] -i inputfile > ... \n"; foreach (@Options) { printf " --%-13s %s%s.\n",$_->{OPT},$_->{DESC}, defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : ""; } exit(1); }