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lib/Bio/NEXUS/Import.pm  view on Meta::CPAN

           detect the correct format. NEXUS files are parsed with
           Bio::NEXUS->read_file();
 Returns : None
 Args    : $filename,  optional: $fileformat, $verbose. 


=head1 DIAGNOSTICS


=over

=item C<< ERROR: $filename is not a valid filename. >>

The file you have specified in L</"new"> or L</"import_file"> does not exist.

=item C<< ERROR: $fileformat is not supported. >>

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

=item C<< 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 L<"APPENDIX: SUPPORTED FILE FORMATS"> for valid PHYLIP files.

=item C<< 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 L<"APPENDIX: SUPPORTED FILE FORMATS"> for valid PHYLIP files.

=item C<< 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.


=item C<< 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.


=back


=head1 CONFIGURATION AND ENVIRONMENT

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


=head1 DEPENDENCIES


L<Bio::NEXUS> 


=head1 INCOMPATIBILITIES

None reported.

=head1 BUGS AND LIMITATIONS


No bugs have been reported.

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

=head1 SEE ALSO

L<Bio::NEXUS>, L<Bio::Phylo>.

The PHYLIP program C<seqboot> can also convert a PHYLIP molecular
sequences or discrete characters morphology data file into the NEXUS format.


=head1 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.

=over

=item C<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


=item C<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


=item C<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

=item C<PHYLIP_DIST_LOWER_BLANK>


        5