NAME

Bio::AlignIO::phylip - PHYLIP format sequence input/output stream

SYNOPSIS

# 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);
    }

DESCRIPTION

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.

FEEDBACK

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/

AUTHORS - Heikki Lehvaslaiho and Jason Stajich

Email: heikki@ebi.ac.uk Email: jason@bioperl.org

APPENDIX

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)