Bio::AlignIO::phylip - PHYLIP format sequence input/output stream
# Do not use this module directly. Use it via the Bio::AlignIO class.
use Bio::AlignIO; use Bio::SimpleAlign; #you can set the name length to something other than the default 10 #if you use a version of phylip (hacked) that accepts ids > 10 my $phylipstream = new Bio::AlignIO(-format => 'phylip', -fh => \*STDOUT, -idlength=>30); # convert data from one format to another my $gcgstream = new Bio::AlignIO(-format => 'msf', -file => 't/data/cysprot1a.msf'); while( my $aln = $gcgstream->next_aln ) { $phylipstream->write_aln($aln); } # do it again with phylip sequential format format $phylipstream->interleaved(0); # can also initialize the object like this $phylipstream = new Bio::AlignIO(-interleaved => 0, -format => 'phylip', -fh => \*STDOUT, -idlength=>10); $gcgstream = new Bio::AlignIO(-format => 'msf', -file => 't/data/cysprot1a.msf'); while( my $aln = $gcgstream->next_aln ) { $phylipstream->write_aln($aln); }
This object can transform Bio::SimpleAlign objects to and from PHYLIP interleaved format. It will not work with PHYLIP sequencial format.
This module will output PHYLIP sequential format. By specifying the flag -interleaved => 0 in the initialization the module can output data in interleaved format.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/
Email: heikki@ebi.ac.uk Email: jason@bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $alignio = new Bio::AlignIO(-format => 'phylip' -file => '>file', -idlength => 10, -idlinebreak => 1); Function: Initialize a new L<Bio::AlignIO::phylip> reader or writer Returns : L<Bio::AlignIO> object Args : [specific for writing of phylip format files] -idlength => integer - length of the id (will pad w/ spaces if needed) -interleaved => boolean - whether or not write as interleaved or sequential format -linelength => integer of how long a sequence lines should be -idlinebreak => insert a line break after the sequence id so that sequence starts on the next line
Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Throws an exception if trying to read in PHYLIP sequential format. Returns : L<Bio::SimpleAlign> object Args :
Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in MSF format Returns : 1 for success and 0 for error Args : L<Bio::Align::AlignI> object
Title : interleaved Usage : my $interleaved = $obj->interleaved Function: Get/Set Interleaved status Returns : boolean Args : boolean
Title : idlength Usage : my $idlength = $obj->interleaved Function: Get/Set value of id length Returns : string Args : string
Title : line_length Usage : $obj->line_length($newval) Function: Returns : value of line_length Args : newvalue (optional)
Title : id_linebreak Usage : $obj->id_linebreak($newval) Function: Returns : value of id_linebreak Args : newvalue (optional)
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.