Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::AlignIO::phylip(3User Contributed Perl DocumentatiBio::AlignIO::phylip(3)

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)

perl v5.32.1			  2019-12-07	       Bio::AlignIO::phylip(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHORS - Heikki Lehvaslaiho and Jason Stajich | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::AlignIO::phylip&sektion=3&manpath=FreeBSD+13.0-RELEASE+and+Ports>

home | help