The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
Bio-NEXUS-Import-v0.0.1
River stage zero No dependents
/ Bio::NEXUS::Import

NAME

Bio::NEXUS::Import - Extends Bio::NEXUS with parsers for file formats of popular phylogeny programs

VERSION

This document describes Bio::NEXUS::Import version 0.0.1

SYNOPSIS

use Bio::NEXUS::Import;

# a PHYLIP-TO-NEXUS converter:
#
# load a PHYLIP file
my $nexus = Bio::NEXUS::Import->new('example.phy');

# and write it as NEXUS formatted file
$nexus->write('example.nex');

DESCRIPTION

A module that extends Bio::NEXUS with parsers for file formats of popular phylogeny programs.

INTERFACE

new

Title   : new
Usage   : Bio::NEXUS::Import->new($filename, $fileformat, $verbose);
Function: If $filename is defined, then this function calls import_file 
Returns : an Bio::NEXUS object
Args    : $filename, $fileformat, $verbose, or none
See also: import_file for a list of supported fileformats, for examples see
          APPENDIX: SUPPORTED FILE FORMATS.

import_file

Title   : import_file
Usage   : Bio::NEXUS::Import->import_file($filename, $fileformat, $verbose);
Function: Reads the contents of the specified file and populate the data 
          in the Bio::NEXUS object.
          Supported fileformats are NEXUS, PHYLIP_DIST_SQUARE, PHYLIP_DIST_LOWER,
          PHYLIP_SEQ_INTERLEAVED, PHYLIP_SEQ_SEQUENTIAL.
          If $fileformat is not defined, then this function tries to
          detect the correct format. NEXUS files are parsed with
          Bio::NEXUS->read_file();
Returns : None
Args    : $filename,  optional: $fileformat, $verbose.

DIAGNOSTICS

ERROR: $filename is not a valid filename.

The file you have specified in "new" or "import_file" does not exist.

ERROR: $fileformat is not supported.

The fileformat you have specified in "new" or "import_file" is not supported. See "APPENDIX: SUPPORTED FILE FORMATS" for a list of supported formats.

Could not import $filename: first line must contain number of taxa.

You tried to import a file with the PHYLIP parser but the file does not look like a PHYLIP file. See "APPENDIX: SUPPORTED FILE FORMATS" for valid PHYLIP files.

Could not import $filename: first line must contain number of characters.

You tried to import a file with the PHYLIP parser for sequence data but the file does not look like a PHYLIP file. See "APPENDIX: SUPPORTED FILE FORMATS" for valid PHYLIP files.

ERROR: Could not parse $filename. Number taxa not correct.

There are taxa in the PHYLIP file than specified in the header. Check your input file.

ERROR: Could not detect file format.

You haven't specified a file format and Bio::NEXUS::Import could not detect the format of your file.

CONFIGURATION AND ENVIRONMENT

Bio::NEXUS::Import requires no configuration files or environment variables.

DEPENDENCIES

Bio::NEXUS

INCOMPATIBILITIES

None reported.

BUGS AND LIMITATIONS

No bugs have been reported.

Please report any bugs or feature requests to bug-bio-nexus-import@rt.cpan.org, or through the web interface at http://rt.cpan.org.

APPENDIX: SUPPORTED FILE FORMATS

Below a collection of examples of all supported file formats:

PHYLIP_DIST_SQUARE
    5
Alpha      0.000 1.000 2.000 3.000 3.000
Beta       1.000 0.000 2.000 3.000 3.000
Gamma      2.000 2.000 0.000 3.000 3.000
Delta      3.000 3.000 0.000 0.000 1.000
Epsilon    3.000 3.000 3.000 1.000 0.000
PHYLIP_DIST_LOWER
    5
Alpha      
Beta       1.00
Gamma      3.00 3.00
Delta      3.00 3.00 2.00
Epsilon    3.00 3.00 2.00 1.00
PHYLIP_SEQ_INTERLEAVED
5    42
Turkey    AAGCTNGGGC ATTTCAGGGT
Salmo gairAAGCCTTGGC AGTGCAGGGT
H. SapiensACCGGTTGGC CGTTCAGGGT
Chimp     AAACCCTTGC CGTTACGCTT
Gorilla   AAACCCTTGC CGGTACGCTT

GAGCCCGGGC AATACAGGGT AT
GAGCCGTGGC CGGGCACGGT AT
ACAGGTTGGC CGTTCAGGGT AA
AAACCGAGGC CGGGACACTC AT
AAACCATTGC CGGTACGCTT AA
PHYLIP_SEQ_SEQUENTIAL
5    42
Turkey    AAGCTNGGGC ATTTCAGGGT
GAGCCCGGGC AATACAGGGT AT
Salmo gairAAGCCTTGGC AGTGCAGGGT
GAGCCGTGGC CGGGCACGGT AT
H. SapiensACCGGTTGGC CGTTCAGGGT
ACAGGTTGGC CGTTCAGGGT AA
Chimp     AAACCCTTGC CGTTACGCTT
AAACCGAGGC CGGGACACTC AT
Gorilla   AAACCCTTGC CGGTACGCTT
AAACCATTGC CGGTACGCTT AA

AUTHOR

Markus Riester <mriester@gmx.de>

LICENCE AND COPYRIGHT

Copyright (c) 2007, Markus Riester <mriester@gmx.de>. All rights reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See perlartistic.

DISCLAIMER OF WARRANTY

BECAUSE THIS SOFTWARE IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE SOFTWARE, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE SOFTWARE "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS WITH YOU. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR, OR CORRECTION.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE SOFTWARE AS PERMITTED BY THE ABOVE LICENCE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE SOFTWARE TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.