/ 
Bio-NEXUS-0.76
River stage one • 1 direct dependent • 1 total dependent
/ Bio::NEXUS::Tools::Modifier

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>