--- name: "Bio::Tools::Run::Alignment::Blat" section: "3pm" platform: "linux" package: "libbio-perl-run-perl" version: "1.7.3-13" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Tools::Run::Alignment::Blat" --- # Bio::Tools::Run::Alignment::Blat(3pm) wrapper modules for the Blat program ## NAME Bio::Tools::Run::Alignment::Blat - wrapper modules for the Blat program ## SYNOPSIS ``` use Bio::Tools::Run::Alignment::Blat; my $factory = Bio::Tools::Run::Alignment::Blat->new(-db => $database); # $report is a Bio::SearchIO-compliant object my $report = $factory->run($seqobj); ``` ## DESCRIPTION Wrapper module for Blat program. This newer version allows for all parameters to be set by passing them as an option to **new()**. 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. ## 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 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 ``` ### 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: ``` http://redmine.open-bio.org/projects/bioperl/ ``` ## AUTHOR ``` Chris Fields - cjfields at bioperl dot org Original author - Bala Email bala@tll.org.sg ``` ## APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_ ### new ``` Title : new Usage : $blat->new( -db => '' ) Function: Create a new Blat factory Returns : A new Bio::Tools::Run::Alignment::Blat object Args : -db : Mandatory parameter. See db() -qsegment : see qsegment() -tsegment : see tsegment() Also, Blat parameters and flags are accepted: -t, -q, -minIdentity, -minScore, -out, -trimT, ... See Blat's manual for details. ``` ### program\_name ``` Title : program_name Usage : $factory->program_name() Function: Get 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 : ``` ### run ``` Title : run() Usage : $obj->run($query) Function: Run Blat. Returns : A Bio::SearchIO object that holds the results Args : A Bio::PrimarySeqI object or a file of query sequences ``` ### align ``` Title : align Usage : $obj->align($query) Function: Alias to run() ``` ### db ``` Title : db Usage : $obj->db() Function: Get or set the file of database sequences (.fa , .nib or .2bit) Returns : Database filename Args : Database filename ``` ### qsegment ``` Title : qsegment Usage : $obj->qsegment('sequence_a:0-1000') Function : pass in a B string for the query sequence(s) Returns : string Args : string 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). ``` ### tsegment ``` Title : tsegment Usage : $obj->tsegment('sequence_a:0-1000') Function : pass in a B string for the target sequence(s) Returns : string Args : string 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). ``` ### outfile\_name ``` Title : outfile_name Usage : $obj->outfile_name('out.blat') Function : Get or set the name for the BLAT output file Returns : string Args : string ``` ### searchio ``` 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 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 ``` ## Bio::ParameterBaseI-specific methods These methods are part of the Bio::ParameterBaseI interface ### set\_parameters ``` 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 ``` ### reset\_parameters ``` 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 ``` ### validate\_parameters ``` Title : validate_parameters Usage : $pobj->validate_parameters(1); Function: sets a flag indicating whether to validate parameters via set_parameters() or reset_parameters() Returns : Bool Args : [optional] value evaluating to True/False Note : NYI ``` ### parameters\_changed ``` Title : parameters_changed Usage : if ($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 ``` ### available\_parameters ``` 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 ``` ### get\_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 ``` ## to\_\* methods All to\_\* methods are implementation-specific ### to\_exe\_string ``` Title : to_exe_string Usage : $string = $pobj->to_exe_string; Function: Returns string (command line string in this case) Returns : String Args : ```