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.

Reporting Bugs
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 _

new
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

next_aln
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 :

write_aln
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

interleaved
Title : interleaved Usage : my $interleaved = $obj->interleaved Function: Get/Set Interleaved status Returns : boolean Args : boolean

idlength
Title : idlength Usage : my $idlength = $obj->interleaved Function: Get/Set value of id length Returns : string Args : string

line_length
Title : line_length Usage : $obj->line_length($newval) Function: Returns : value of line_length Args : newvalue (optional)

id_linebreak
Title : id_linebreak Usage : $obj->id_linebreak($newval) Function: Returns : value of id_linebreak Args : newvalue (optional)