Bio::Tools::Run::Alignment::Blat
Build a Blat factory.
use Bio::Tools::Run::Alignment::Blat; my $factory = Bio::Tools::Run::Alignment::Blat->new(); # Pass the factory a Bio::Seq object # @feats is an array of Bio::SeqFeature::Generic objects my @feats = $factory->run($seq,$DB);
Wrapper module for Blat program. This newer version allows for all parameters to be set.
Key bits not implemented yet (TODO):
Implement all needed Bio::Tools::Run::WrapperBase methods
Missing are a few, including version().
Re-implement using IPC::Run
Would like to get this running under something less reliant on OS-dependent changes within code.
No .2bit or .nib conversions yet
These require callouts to faToNib or faTwoTwoBit, which may or may not be installed on a user's machine. We can possibly add functionality to check for faToTwoBit/faToNib and other UCSC tools in the future.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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.
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:
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Chris Fields - cjfields at bioperl dot org Original author- Bala Email bala@tll.org.sg
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : $blat->new(@params) Function: creates a new Blat factory Returns : Bio::Tools::Run::Alignment::Blat Args :
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 :
Title : run() Usage : $obj->run($query) Function: Runs Blat and creates an array of featrues Returns : An array of Bio::SeqFeature::Generic objects Args : A Bio::PrimarySeqI or a file name
Title : align Usage : $obj->align($query) Function: Alias to run()
Title : qsegment Usage : $obj->qsegment('sequence_a:0-1000') Function : pass in a B<UCSC-compliant> string for the query sequence(s) Returns : string Args : string Status : New Note : Requires the sequence(s) in question be 2bit or nib format Reminder : UCSC segment/regions coordinates are 0-based half-open (sequence begins at 0, but start isn't counted with length), whereas BioPerl coordinates are 1-based closed (sequence begins with 1, both start and end are counted in the length of the segment). For example, a segment that is 'sequence_a:0-1000' will have BioPerl coordinates of 'sequence_a:1-1000', both with the same length (1000).
Title : tsegment Usage : $obj->tsegment('sequence_a:0-1000') Function : pass in a B<UCSC-compliant> string for the target sequence(s) Returns : string Args : string Status : New Note : Requires the sequence(s) in question be 2bit or nib format Reminder : UCSC segment/regions coordinates are 0-based half-open (sequence begins at 0, but start isn't counted with length), whereas BioPerl coordinates are 1-based closed (sequence begins with 1, both start and end are counted in the length of the segment). For example, a segment that is 'sequence_a:0-1000' will have BioPerl coordinates of 'sequence_a:1-1000', both with the same length (1000).
Title : searchio Usage : $obj->searchio{-writer => $writer} Function : Pass in additional parameters to the returned Bio::SearchIO parser Returns : Hash reference with Bio::SearchIO parameters Args : Hash reference Status : New Note : Currently, this implementation overrides any passed -format parameter based on whether the output is changed ('out'). This may change if requested, but we can't see the utility of doing so, as requesting mismatched output/parser combinations is just a recipe for disaster
These methods are part of the Bio::ParameterBaseI interface
Title : set_parameters Usage : $pobj->set_parameters(%params); Function: sets the parameters listed in the hash or array Returns : None Args : [optional] hash or array of parameter/values. These can optionally be hash or array references Note : This only sets parameters; to set methods use the method name
Title : reset_parameters Usage : resets values Function: resets parameters to either undef or value in passed hash Returns : none Args : [optional] hash of parameter-value pairs
Title : validate_parameters Usage : $pobj->validate_parameters(1); Function: sets a flag indicating whether to validate parameters via set_parameters() or reset_parameters() Returns : Bool Args : [optional] value evaluating to True/False Note : NYI
Title : parameters_changed Usage : if ($pobj->parameters_changed) {...} Function: Returns boolean true (1) if parameters have changed Returns : Boolean (0 or 1) Args : None Note : This module does not run state checks, so this always returns True
Title : available_parameters Usage : @params = $pobj->available_parameters() Function: Returns a list of the available parameters Returns : Array of parameters Args : [optional] name of executable being used; defaults to returning all available parameters
Title : get_parameters Usage : %params = $pobj->get_parameters; Function: Returns list of set key-value pairs, parameter => value Returns : List of key-value pairs Args : none
All to_* methods are implementation-specific
Title : to_exe_string Usage : $string = $pobj->to_exe_string; Function: Returns string (command line string in this case) Returns : String Args :
To install Bio::DB::ESoap, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::DB::ESoap
CPAN shell
perl -MCPAN -e shell install Bio::DB::ESoap
For more information on module installation, please visit the detailed CPAN module installation guide.