Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

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

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::AlignIO class.

       This example shows how to write to phylip format:

           use Bio::AlignIO;
           use Bio::SimpleAlign;

           # Use -idlength to set the name length to something other than
           # the default 10 if you need longer ids.
           my $phylipstream = Bio::AlignIO->new(-format   => 'phylip',
                                                -fh       => \*STDOUT,
                                                -idlength => 30);
           # Convert data from one format to another
           my $gcgstream = Bio::AlignIO->new(-format => 'msf',
                                             -file   => 't/data/cysprot1a.msf');

           while( my $aln = $gcgstream->next_aln ) {
               $phylipstream->write_aln($aln);
           }

           # With phylip sequential format format
           $phylipstream->interleaved(0);
           # Or initialize the object like this
           $phylipstream = Bio::AlignIO->new(-interleaved => 0,
                                             -format      => 'phylip',
                                             -fh          => \*STDOUT,
                                             -idlength    => 20 );
           $gcgstream = Bio::AlignIO->new(-format => 'msf',
                                          -file   => 't/data/cysprot1a.msf');

           while( my $aln = $gcgstream->next_aln ) {
               $phylipstream->write_aln($aln);
           }

       This example shows how to read phylip format:

           my $in = Bio::AlignIO->new(
             -file        => $inFile,
             -format      => 'phylip',
             -interleaved => 0,
             -longid      => 1
           );

           my $out = Bio::AlignIO->new(
             -file   => ">$outFile",
             -format => 'fasta'
           );

           while ( my $aln = $in->next_aln() ) {
             $out->write_aln($aln);
           }

       The -longid argument is required if the input phylip format file has ids with lengths
       greater then 10 characters.

DESCRIPTION

       This object can transform Bio::SimpleAlign objects to and from PHYLIP format. By default
       it works with the interleaved format. By specifying the flag -interleaved => 0 in the
       initialization the module can read or write data in sequential format.

       Reading phylip format with long IDs up to 50 characters is supported by the flag -longid
       =>1. ID strings can be surrounded by single quotes.  They are mandatory only if the IDs
       contain spaces.

FEEDBACK

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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 the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHORS - Heikki Lehvaslaiho and Jason Stajich

       Email: heikki at ebi.ac.uk Email: jason at 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 = Bio::AlignIO->new(-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) when writing phylip
                  -interleaved => boolean - whether interleaved
                                  or sequential format required
                  -line_length  => 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
                  -flag_SI => whether or not write a "S" or "I" just after
                              the num.seq. and line len., in the first line
                  -tag_length => integer of how long the tags have to be in
                                each line between the space separator. set it
                                to 0 to have 1 tag only.
                  -wrap_sequential => boolean for whether or not sequential
                                      format should be broken up or a single line
                                      default is false (single line)
                  -longid => boolean to read arbitrary long IDs (default is false)

   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 phylip 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

   flag_SI
        Title   : flag_SI
        Usage   : my $flag = $obj->flag_SI
        Function: Get/Set if the Sequential/Interleaved flag has to be shown
                  after the number of sequences and sequence length
        Example :
        Returns : boolean
        Args    : boolean

   idlength
        Title   : idlength
        Usage   : my $idlength = $obj->idlength
        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)

   tag_length
        Title   : tag_length
        Usage   : $obj->tag_length($newval)
        Function:
        Example : my $tag_length = $obj->tag_length
        Returns : value of the length for each space-separated tag in a line
        Args    : newvalue (optional) - set to zero to have one tag per line

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

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

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