File Coverage

bin/biotree

Criterion	Covered	Total	%
statement	36	36	100.0
branch	3	6	50.0
condition			n/a
subroutine	10	10	100.0
pod			n/a
total	49	52	94.2

#!/usr/bin/env perl
use strict;
use warnings;
use v5.10;

use Path::Tiny;
use lib path($0)->absolute->parent->sibling('lib')->stringify;
use Pod::Usage;
use Getopt::Long qw( :config bundling permute no_getopt_compat );

use Bio::BPWrapper;
use Bio::BPWrapper::TreeManipulations;

use constant PROGRAM => File::Basename::basename(__FILE__);

####################### Option parsing ######################
pod2usage(1) if scalar(@ARGV) < 1;
my %opts;
GetOptions(\%opts,
	   "help|h",
	   "man",
	   "version|V",
	   "as-text|t", # for preview text tree
	   "ci|c=s", # attach binary trait table
	   "clean-br|b",
	   "clean-boot|B",
	   "cut-tree=f", # cut tree to identify groups
	   "cut-sis=i", # identify sister node with fewer than i descendants
	   "del-otus|d=s",
	   "del-low-boot|D=f",
	   "del-short-br|E=f",
	   "depth=s",
	   "dist=s",
	   "dist-all",
	   "ead", # edge-length abundance distribution; O'Dwyer et al. PNAS (2015)
	   "input|i=s",
	   "ids-all",
	   "label-nodes",
	   "label-selected-nodes=s", # based on a file
	   "lca=s",
	   "length|l",
	   "length-all|L",
	   "ltt=s",
	   "mid-point|m",
	   "multi2bi",
	   "otus-all|u",
	   "otus-desc|U:s",
	   "otus-num|n",
	   "output|o=s",
	   "random=i",
	   "ref=s", # specify reference OTU (move to top)
	   "rename-tips=s",
	   "reroot|r=s",
 	   "rotate-node=s", # rotate around an internal node (give node id)
	   "sis-pairs", # pairwise OTU togetherness
#	   "sort-child=s", # sort child by height (default) or others (to make output tree consistent)
	   "subset|s=s",
	   "swap-otus=s", # ??
	   "tips-to-root",
	   "tree-shape", # for apTreeshape package
	   "trim-tips=f",
	   "walk|w=s",
	   "walk-edge=s",
#	   "rmbl|R",
#          "bootclean|b:f",
#          "collapse|c=s@",
#          "getroot|g",
#          "prune|p=s@",
#          "compnames|x",
#	   "collabel|C:s",
#	   "tree2tableid|I:s",
#	   "joindata|J=s@",
#	   "rename|N",
#	   "tree2table|T",
#          "comptrees|X",
	  ) or pod2usage(2);

Bio::BPWrapper::print_version(PROGRAM) if $opts{"version"};

# Create a new BioTree object and initialize that.
unshift @ARGV, \%opts;
initialize(@ARGV);
write_out(\%opts);

################# POD Documentation ##################
__END__