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Bio::NEXUS::Tools::NexUserfContributed Perl DBio::NEXUS::Tools::NexModifier(3)

   new
	Title	: new
	Usage	: NA
	Function: create a new modifier	object
	Returns	: NA
	Args	: NA

   modify
	Title	: modify
	Usage	: NA
	Function: alter	object
	Returns	: NA
	Args	: NA

   rename_otus
	Title	: rename_otus
	Usage	: NA
	Function: assigns new labels to	OTUs
	Returns	: NA
	Args	: NA

   selectbyblock
	Title	: selectbyblock
	Usage	: NA
	Function: select a subset of blocks
	Returns	: NA
	Args	: NA

   selectbyotu
	Title	: selectbyotu
	Usage	: NA
	Function: select subset	of OTUs	by labels
	Returns	: NA
	Args	: NA

   selectbytree
	Title	: selectbytree
	Usage	: NA
	Function: select a tree
	Returns	: NA
	Args	: NA

   selectbyinode
	Title	: selectbyinode
	Usage	: NA
	Function: select a subtree by specifying its root internal node
	Returns	: NA
	Args	: NA

   selectbycolumn
	Title	: selectbycolumn
	Usage	: NA
	Function: select ($command=1) or exclude ($command=0) specified	column list or file with list
	Returns	: NA
	Args	: NA

   selectbysets
	Title	: selectbysets
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   parse_number
	Title	: parse_number
	Usage	: NA
	Function: parse	numbers	in format "1-3,	4 6 8-10"
	Returns	: NA
	Args	: NA

   unquote
	Title	: unquote
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   exclude_blocks
	Title	: exclude_blocks
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   exclude_subtree
	Title	: exclude_subtree
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   reroottree
	Title	: reroottree
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   addtree
	Title	: addtree
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   setsbyfile
	Title	: setsbyfile
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   setsbyinode
	Title	: setsbyinode
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   setsbyclade
	Title	: setsbyclade
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   setsbyotus
	Title	: setsbyotus
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   setsbyunion
	Title	: setsbyunion
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   setsbydifference
	Title	: setsbydifference
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   setsbycharstate
	Title	: setsbycharstate
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   parse_charstate_args
	Title	: parse_charstate_args
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   setsbycladeconsensus
	Title	: setsbycladeconsensus
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   set_consensus_seqs
	Title	: set_consensus_seqs
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   simplify_tree
	Title	: simplify_tree
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   validate_otus
	Title	: validate_otus
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   add_or_create_set
	Title	: add_or_create_set
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   removesets
	Title	: removesets
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   swap_children
	Title	: swap_children
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   listsets
	Title	: listsets
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   listsetnames
	Title	: listsetnames
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   open_filehandle
	Title	: open_filehandle
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   get_setsblock_if_setsblock
	Title	: get_setsblock_if_setsblock
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

   file_overwrite_warning
	Title	: file_overwrite_warning
	Usage	: NA
	Function: NA
	Returns	: NA
	Args	: NA

NAME
       Bio::NEXUS::Tools::Modifier - NEXUS file	content	modifier (
       exclude/select/rename options on	OTUs).

SYNOPSIS
       nextool.pl <input_file> [output_file] [COMMAND [arguments]]

       if outfile is not specified, just read input file and output to
       temp.nex

       Commands:

	   rewrite
	   rename_otus <translation_file>
	   reroot <outgroup_node_name> [tree_name]
	   select blocks <block1 block2	...>
	   select OTU <OTU_1 OTU_2 ...>	or <-f filename>
	   select tree <tree_name>
	   select subtree <inode_number> [tree_name]
	   select column <columns> or <-f filename>
	   exclude blocks <block1 block2 ...>
	   exclude OTU <otu1 otu2 ...>
	   exclude subtree <inode> [treename]
	   exclude column <columns> or <-f filename>
	   makesets byfile <file1> [file2 file3	...]
	   makesets byinode <inode1> [inode2 inode3 ...]
	   makesets byclade <OTU1> <OTU2> [OTU3	OTU4 ...]
	       Square brackets are required syntax in this command:
	   makesets byotus <set1>=[<OTU1 OTU2 ...>] <set2>=[<OTU3 OTU4 ...>] ...
	       Square brackets are required in this command:
	   makesets byunion <set1>=[<setA + setB ...>] <set2>=[<setA + setC ...>] ...
	       Square brackets are required in this command:
	   makesets bydifference <set1>=[<setA - setB>]	<set2>=[<setA -	setC>] ...
	       Square brackets around 'state' argument are required in this command:
	   makesets bycharstate	[title=char_block_title] [set1=]"<sequence_or_intron_position>[<state>]" [set2=...]
	   makesets bycladeconsensus [title=char_block_title]
	   removesets <set1 set2 ...>
	   listsets [set1 set2 ...]
	   listsetnames
	   renamesets oldname1 newname1	[oldname2 newname2 ...]

COMMANDS
   rewrite
       Writes the contents of <input_file> to <output_file>.  This is used to
       standardize the format of the file.  this is the	default	program	action
       if <outfile> is not specified, the output file will be temp.nex

   rename_otus <translation_file>
       Renames OTUs in taxa, characters	and trees blocks according to
       translation_file. Each line of translation_file contains	the old	name,
       separated by whitespace,	then the new name.

   reroot <outgroup_node_name> [tree_name]
       reroot the tree of tree_name (optional--	the first tree in trees	block
       if not specified) with outgroup_node_name as the	new outgroup

   select blocks <block1 block2	...>
       Select block given in list

   select OTU <OTU_1 OTU_2 ...>	or <-f filename>
       Selects OTUs given in list. Changes taxa	block, characters block	and
       trees block.

   select tree <tree_name>
       Selects one tree	given the tree name. Changes taxa/characters blocks to
       match.

   select subtree <inode_number> [tree_name]
       Selects subtree given the tree name and the internal node number.
       Changes taxa/characters blocks to match.

   select column <columns> or <-f filename>
       Selects a number	of columns from	character lists	to get a new set of
       character lists (for a new Bio::NEXUS file). eg,	"1-3, 5	8, 10-15"
       (comma or space can be used to separate numbers)

   exclude blocks <block1 block2 ...>
       Remove blocks from file

   exclude OTU <otu1 otu2 ...>
       Remove OTUs from	file

   exclude subtree <inode> [treename]
       Remove subtree rooted with 'inode' in 'treename'	or the first tree if
       'treename' is not specified

   exclude column <columns> or <-f filename>
       Remove a	number of columns from character lists to get a	new set	of
       character lists (for a new Bio::NEXUS file). eg,	"1-3, 5	8, 10-15"
       (comma or space can be used to separate numbers)

   makesets byfile <file1> [file2 file3	...]
       Add sets	based on OTU's listed in simple	text files.  Sets take names
       of files; OTU's should be newline-delimited in the text files.

   makesets byinode <inode1> [inode2 inode3 ...]
       Add sets	based on ancestral internal nodes and their children

   makesets byclade <OTU1> <OTU2> [OTU3	OTU4 ...]
       Add sets	by finding the children	of the most recent common ancestor
       (mrca) of OTU1 and OTU2 pairs

   makesets byotus <set1>=[<OTU1 OTU2 ...>] <set2>=[<OTU3 OTU4 ...>] ...
       Add sets	by specifying setnames and OTU's each set is to	contain.
       Syntax is setname=[<OTU LIST>]

   makesets byunion <set1>=[<setA + setB ...>] <set2>=[<setA + setC ...>] ...
       Add sets	by specifying setnames and which existing sets contain the
       OTUs the	new set	will comprise.	Syntax is setname=[<SET	LIST>]

   makesets bydifference <set1>=[<setA - setB>]	<set2>=[<setA -	setC>] ...
       Add sets	by specifying setnames and which existing sets contain the
       OTUs that will be used in defining the new sets.

   makesets bycharstate	[title=char_block_title]
       [set1=]"<sequence_or_intron_position>[<state>]" [set2=...]
       Add sets	by specifying setnames and which existing sets contain the
       OTUs that will be used in defining the new sets.

   makesets bycladeconsensus [title=char_block_title]
       Add sets	by finding clades that have a consensus	sequence at all	loci,
       and creating one	set for	each group of "otu synonyms"

   removesets [-p] set1	set2 ...
       Delete sets from	NEXUS file.  Will empty	SETS Block but not remove it
       from file. '-p' switch allows you to specify regular expression
       patterns	('set\d*' will delete all sets of the form set<number>.)
       QUOTATION MARKS AROUND PATTERNS IS STRONGLY RECOMMENDED.

   listsets
       Print sets (all sets by default,	otherwise those	provided by user) to
       output file, or standard	out of STDOUT or - is used as output filename

   listsetnames
       Print setnames to output	file, or standard out if STDOUT	or - is	used
       as output filename

   renamesets oldname1 newname1	[oldname2 newname2 ...]
       Rename sets by space-delimited <oldname newname>	pairs

DESCRIPTION
       This program provides several services in the manipulation of NEXUS
       files (selecting	specific OTUs or tree nodes, combining files, renaming
       OTUs, etc.

VERSION
       $Revision: 1.2 $

REQUIRES
       Bio::NEXUS

AUTHOR
       Chengzhi	Liang <liangc@umbi.umd.edu> Peter Yang <pyang@rice.edu>	Tom
       Hladish <hladish@umbi.umd.edu>

perl v5.32.0			  2008-06-16 Bio::NEXUS::Tools::NexModifier(3)

NAME | SYNOPSIS | COMMANDS | DESCRIPTION | VERSION | REQUIRES | AUTHOR

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