GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::NEXUS::TOOLS::NEXMODIFIER (3)

.ds Aq ’

    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).

CONTENTS

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

<B>This programB> 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>
Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::NEXUS::TOOLS::NEXMODIFIER (3) 2008-06-16

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.