/ 
BioPerl-1.007000_005
River stage two • 60 direct dependents • 65 total dependents
/ Bio::AlignIO::phylip

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 = 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);
}

# do it again with phylip sequential format format
$phylipstream->interleaved(0);
# can also initialize the object like this
$phylipstream = Bio::AlignIO->new(-interleaved => 0,
                                 -format => 'phylip',
                                 -fh   => \*STDOUT,
                                 -idlength=>10);
$gcgstream     =  Bio::AlignIO->new(-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 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.

Long IDs up to 50 characters are supported by flag -longid => 1. ID strings can be surrounded by single quoted. 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)
           -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 for allowing 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)