Bio::Tools::Run::Phylo::Phast::PhastCons man page on Pidora

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Bio::Tools::Run::PhyloUseraContribuBio::Tools::Run::Phylo::Phast::PhastCons(3)

NAME
       Bio::Tools::Run::Phylo::Phast::PhastCons - Wrapper for footprinting
       using
						  phastCons

SYNOPSIS
	 use Bio::Tools::Run::Phylo::Phast::PhastCons;

	 # Make a PhastCons factory
	 $factory = Bio::Tools::Run::Phylo::Phast::PhastCons->new();

	 # Pass the factory an alignment and the corresponding species tree
	 $align_filename = 't/data/apes.multi_fasta';
	 $species_tree_filename = 't/data/apes.newick';
	 @features = $factory->run($align_filename, $species_tree_filename);

	 # or get a Bio::Align::AlignI (SimpleAlign) object from somewhere, and
	 # generate the species tree automatically using a Bio::DB::Taxonomy database
	 $tdb = Bio::DB::Taxonomy->new(-source => 'entrez');
	 @features = $factory->run($aln_obj, $tdb);

	 # @features is an array of Bio::SeqFeature::Annotated, one feature per
	 # alignment sequence and prediction

DESCRIPTION
       This is a wrapper for running the phastCons application by Adam Siepel.
       You can get details here:
       http://compgen.bscb.cornell.edu/~acs/software.html phastCons is used
       for phylogenetic footprinting/ shadowing.

       Currently the interface is extremely simplified, allowing only one
       analysis method. The focus here is on ease of use, allowing phastCons
       to estimate as many parameters as possible and having it output just
       the 'most conserved' blocks it detects. You can, however, try supplying
       normal phastCons arguments to new(), or calling arg-named methods
       (excluding initial hyphens and converting others to underscores, eg.
       $factory->indels_only(1) to set the --indels-only arg).

       The particular analysis carried out here is to:

	1. Use phyloFit to generate a tree model for initialization of the nonconserved
	   model from the supplied alignment (all data) and species tree
	2. Run phastCons in 'training' mode for parameter estimation using all the
	   alignment data and the model from step 1
	3. Run phastCons with the trees from step 2 to discover the most conserved
	   regions

       See the 'HowTo' at
       http://compgen.bscb.cornell.edu/~acs/phastCons-HOWTO.html for details
       on how to improve results.

       WARNING: the API is likely to change in the future to allow for
       alternative analysis types.

       You will need to enable this phastCons wrapper to find the phast
       programs (at least phastCons and phyloFit).  This can be done in (at
       least) three ways:

	1. Make sure the phastCons and phyloFit executables are in your path.
	2. Define an environmental variable PHASTDIR which is a
	   directory which contains the phastCons and phyloFit applications:
	   In bash:

	   export PHASTDIR=/home/username/phast/bin

	   In csh/tcsh:

	   setenv PHASTDIR /home/username/phast/bin

	3. Include a definition of an environmental variable PHASTDIR in
	   every script that will use this PhastCons wrapper module, e.g.:

	   BEGIN { $ENV{PHASTDIR} = '/home/username/phast/bin' }
	   use Bio::Tools::Run::Phylo::Phast::PhastCons;

FEEDBACK
   Mailing Lists
       User feedback is an integral part of the evolution of this and other
       Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   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 of
       the bugs and their resolution. Bug reports can be submitted via the
       web:

	 http://bugzilla.open-bio.org/

AUTHOR - Sendu Bala
       Email bix@sendu.me.uk

APPENDIX
       The rest of the documentation details each of the object methods.
       Internal methods are usually preceded with a _

   program_name
	Title	: program_name
	Usage	: $factory>program_name()
	Function: holds the program name
	Returns : string
	Args	: None

   program_dir
	Title	: program_dir
	Usage	: $factory->program_dir(@params)
	Function: returns the program directory, obtained from ENV variable.
	Returns : string
	Args	: None

   new
	Title	: new
	Usage	: $factory = Bio::Tools::Run::Phylo::Phast::PhastCons->new(@params)
	Function: Creates a new PhastCons factory
	Returns : Bio::Tools::Run::Phylo::Phast::PhastCons
	Args	: Optionally, provide any of the following (defaults are not to use,
		  see the same-named methods for information on what each option does):
		  {
		   -target_coverage  => number between 0 and 1
		   AND
		   -expected_length  => int
		  }
		  -rho => number between 0 and 1
		  -quiet => boolean (turn on or off program output to console)

		  Most other options understood by phastCons can be supplied as key =>
		  value pairs in this way. Options that don't normally take a value
		  should be given a value of 1. You can type the keys as you would on
		  the command line (eg. '--indels-only' => 1) or with only a single
		  hyphen to start and internal hyphens converted to underscores (eg.
		  -indels_only => 1) to avoid having to quote the key.

		  These options can NOT be used with this wrapper currently:
		  estimate_trees / T
		  estimate_rho / O
		  gc / G
		  msa_format / i
		  score / s
		  no_post_probs / n
		  seqname / N
		  idpref / P
		  help / h
		  alias / A
		  most_conserved / V / viterbi
		  refidx / r

   target_coverage
	Title	: target_coverage
	Usage	: $factory->target_coverage(0.25);
	Function: Constrain transition parameters such that the expected fraction of
		  sites in conserved elements is the supplied value.
	Returns : number (default undef)
	Args	: None to get, number (between 0 and 1) to set

   expected_length
	Title	: expected_length
	Usage	: $factory->expected_length(5);
	Function: Set transition probabilities such that the expected length of a
		  conserved element is the supplied value. target_coverage() must also
		  be set.
	Returns : int (default undef)
	Args	: None to get, int to set

   rho
	Title	: rho
	Usage	: $factory->rho(0.3);
	Function: Set the *scale* (overall evolutionary rate) of the model for the
		  conserved state to be the supplied number times that of the model for
		  the non-conserved state (default 0.3).
	Returns : number (default undef)
	Args	: None to get, number (between 0 and 1) to set

   run
	Title	: run
	Usage	: $result = $factory->run($fasta_align_file, $newick_tree_file);
		  -or-
		  $result = $factory->run($align_object, $tree_object);
		  -or-
		  $result = $factory->run($align_object, $db_taxonomy_object);
	Function: Runs phastCons on an alignment to find the most conserved regions
		  ('footprinting').
	Returns : array of Bio::SeqFeature::Annotated (one feature per alignment
		  sequence and prediction)
	Args	: The first arguement represents an alignment, the second arguement
		  a species tree.
		  The alignment can be provided as a multi-fasta format alignment
		  filename, or a Bio::Align::AlignI complient object (eg. a
		  Bio::SimpleAlign).
		  The species tree can be provided as a newick format tree filename
		  or a Bio::Tree::TreeI complient object. Alternatively a
		  Bio::DB::Taxonomy object can be supplied, in which case the species
		  tree will be generated by using the alignment sequence names as
		  species names and looking for those in the supplied database.

		  In all cases, the alignment sequence names must correspond to node
		  ids in the species tree. Multi-word species names should be joined
		  with underscores to form the sequence names, eg. Homo_sapiens

   _setparams
	Title	: _setparams
	Usage	: Internal function, not to be called directly
	Function: Creates a string of params to be used in the command string
	Returns : string of params
	Args	: alignment file name for result production, AND filename of phyloFit
		  generated init.mod file to estimate trees

perl v5.14.1			  2Bio::Tools::Run::Phylo::Phast::PhastCons(3)
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