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://redmine.open-bio.org/projects/bioperl/

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 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
           Bio::SimpleAlign).
           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

_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