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       Bio::Tools::Run::Phylo::Phast::PhastCons	- Wrapper for footprinting

	 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

       This is a wrapper for running the phastCons application by Adam Siepel.
       You can get details here: 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

       See the 'HowTo' at 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;

   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.			- General discussion	- About	the mailing lists

       Please direct usage questions or	support	issues to the mailing list:

       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

AUTHOR - Sendu Bala

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

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

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

	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
		   -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

	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

	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

	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

	Title	: run
	Usage	: $result = $factory->run($fasta_align_file, $newick_tree_file);
		  $result = $factory->run($align_object, $tree_object);
		  $result = $factory->run($align_object, $db_taxonomy_object);
	Function: Runs phastCons on an alignment to find the most conserved regions
	Returns	: array	of Bio::SeqFeature::Annotated (one feature per alignment
		  sequence and prediction)
	Args	: The first argument represents	an alignment, the second argument
		  a species tree.
		  The alignment	can be provided	as a multi-fasta format	alignment
		  filename, or a Bio::Align::AlignI compliant object (eg. a
		  The species tree can be provided as a	newick format tree filename
		  or a Bio::Tree::TreeI	compliant 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

	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 v5.24.1			  2Bio::Tools::Run::Phylo::Phast::PhastCons(3)


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