| Bio::Tools::Run::Alignment::Blat(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Alignment::Blat(3pm) |
Bio::Tools::Run::Alignment::Blat - wrapper modules for the Blat program
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);
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):
Missing are a few, including version().
Would like to get this running under something less reliant on OS-dependent changes within code.
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( -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.
Title : program_name Usage : $factory->program_name() Function: Get 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: Run Blat. Returns : A Bio::SearchIO object that holds the results Args : A Bio::PrimarySeqI object or a file of query sequences
Title : align Usage : $obj->align($query) Function: Alias to run()
Title : db Usage : $obj->db() Function: Get or set the file of database sequences (.fa , .nib or .2bit) Returns : Database filename Args : Database filename
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
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
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 : outfile_name
Usage : $obj->outfile_name('out.blat')
Function : Get or set the name for the BLAT output file
Returns : string
Args : string
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
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 :
| 2023-01-22 | perl v5.36.0 |