NAME
Bio::NEXUS::Import - Extends Bio::NEXUS with parsers for file formats of popular phylogeny programs
VERSION
This document describes Bio::NEXUS::Import version 0.1.0
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_SQUARE_BLANK, PHYLIP_DIST_LOWER,
PHYLIP_DIST_LOWER_BLANK, PHYLIP_SEQ_INTERLEAVED,
PHYLIP_SEQ_INTERLEAVED_BLANK, PHYLIP_SEQ_SEQUENTIAL,
PHYLIP_SEQ_SEQUENTIAL_BLANK.
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.
ERROR: 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.
ERROR: 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 is a different number of 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
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.
SEE ALSO
The PHYLIP program seqboot can also convert a PHYLIP molecular sequences or discrete characters morphology data file into the NEXUS format.
APPENDIX: SUPPORTED FILE FORMATS
This appendix lists examples of all supported file formats. The PHYLIP_*_BLANK formats are modifications of the PHYLIP formats to support longer labels than the 10 characters. The end of a label is marked with a white space character such as a blank.
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_SQUARE_BLANK-
5 Alpha_Long_Taxon 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_DIST_LOWER_BLANK-
5 Alpha_Long_Taxon 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
LICENCE AND COPYRIGHT
Copyright (c) 2007-2011, <limaone@cpan.org>.
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.