From Code to Community: Sponsoring The Perl and Raku Conference 2025 Learn more

 / 
BioPerl-1.7.8
River stage two • 60 direct dependents • 64 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.

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)