Bio::AlignIO::phylip(3pm)

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:

[email protected]

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)