NAME¶
Bio::Tools::Run::Alignment::Blat
SYNOPSIS¶
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);
DESCRIPTION¶
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.
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(@params)
Function: creates a new Blat factory
Returns : Bio::Tools::Run::Alignment::Blat
Args :
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 :
run¶
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
align¶
Title : align
Usage : $obj->align($query)
Function: Alias to run()
qsegment¶
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).
tsegment¶
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).
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
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
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 :