Search results for "dist:FAST Bio::SearchIO::blast"
FAST::Bio::SearchIO::blast - Event generator for event based parsing of blast reports
This object encapsulated the necessary methods for generating events suitable for building FAST::Bio::Search objects from a BLAST report file. Read the FAST::Bio::SearchIO for more information about how to use this. This driver can parse: * NCBI prod...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::blast_pull - A parser for BLAST output
This object implements a pull-parser for BLAST output. It is fast since it only does work on request (hence 'pull'). Currently only NCBI BLASTN and BLASTP are supported....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::XML::BlastHandler - XML Handler for NCBI Blast XML parsing.
This is the XML handler for BLAST XML parsing. Currently it passes elements off to the event handler, which is ultimately responsible for FAST::Bio::Search object generation. This was recently split off from the original code for FAST::Bio::SearchIO:...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::XML::PsiBlastHandler - XML Handler for NCBI Blast PSIBLAST XML parsing.
This is the XML handler for BLAST PSIBLAST XML parsing. Currently it passes elements off to the event handler, which is ultimately responsible for FAST::Bio::Search object generation. This was recently split off from the original code for FAST::Bio::...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
This is a driver for instantiating a parser for report files from sequence database searches. This object serves as a wrapper for the format parsers in FAST::Bio::SearchIO::* - you should not need to ever use those format parsers directly. (For peopl...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing.
This object implements a NCBI Blast XML parser. It requires XML::SAX; it is also recommended (for faster parsing) that XML::SAX::ExpatXS or XML::LibXML be installed. Either 'XML::SAX::ExpatXS' or 'XML::LibXML::SAX::Parser' should be set as the defaul...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::BlastUtils - Utility functions for FAST::Bio::Search:: BLAST objects
The BlastUtils.pm module is a collection of subroutines used primarily by FAST::Bio::Search::Hit::BlastHit objects for some of the additional functionality, such as HSP tiling. Right now, the BlastUtils is just a collection of methods, not an object,...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::megablast - a driver module for FAST::Bio::SearchIO to parse megablast reports (format 0)
Beware! Because of the way megablast report format 0 is coded, realize that score means # gap characters + # mismatches for a HSP. The docs from NCBI regarding FORMAT 0 # 0: Produce one-line output for each alignment, in the form # # 'subject-id'=='[...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::SearchUtils - Utility functions for FAST::Bio::Search:: objects
The SearchUtils.pm module is a collection of subroutines used primarily by FAST::Bio::Search::Hit::HitI objects for some of the additional functionality, such as HSP tiling. Right now, the SearchUtils is just a collection of methods, not an object....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::blasttable - Driver module for SearchIO for parsing NCBI -m 8/9 format
This module will support parsing NCBI -m 8 or -m 9 tabular output and WU-BLAST -mformat 2 or -mformat 3 tabular output....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::FastHitEventBuilder - Event Handler for SearchIO events.
This object handles Search Events generated by the SearchIO classes and build appropriate FAST::Bio::Search::* objects from them. This object is intended for lightweight parsers which only want Hits and not deal with the overhead of HSPs. It is a lot...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::bl2seq - bl2seq sequence input/output stream
This object can create FAST::Bio::SimpleAlign sequence alignment objects (of two sequences) from "bl2seq" BLAST reports. A nice feature of this module is that - in combination with FAST::Bio::Tools::Run::StandAloneBlast.pm or a remote BLAST - it can ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AnalysisParserI - Generic analysis output parser interface
AnalysisParserI is a interface for describing generic analysis result parsers. This module makes no assumption about the nature of analysis being parsed, only that zero or more result sets can be obtained from the input source. This module was derive...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::Hit::PullHitI - FAST::Bio::Search::Hit::HitI interface for pull parsers.
This object handles the hit data from a database sequence search. PullHitI is for fast implementations that only do parsing work on the hit data when you actually request information by calling one of the HitI methods. Many methods of HitI are implem...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::gmap_f9 - Event generator for parsing gmap reports (Z format)
This object encapsulated the necessary methods for generating events suitable for building FAST::Bio::Search objects from a GMAP "compressed" report (from gmap run with -Z flag) Read the FAST::Bio::SearchIO for more information about how to use this....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::HSP::PullHSPI - FAST::Bio::Search::HSP::HSPI interface for pull parsers.
PullHSP is for fast implementations that only do parsing work on the hsp data when you actually request information by calling one of the HSPI methods. Many methods of HSPI are implemented in a way suitable for inheriting classes that use FAST::Bio::...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::Hit::HitI - Interface for a hit in a similarity search result
FAST::Bio::Search::Hit::* objects are data structures that contain information about specific hits obtained during a library search. Some information will be algorithm-specific, but others will be generally defined....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::Hit::GenericHit - A generic implementation of the FAST::Bio::Search::Hit::HitI interface
This object handles the hit data from a Database Sequence Search such as FASTA or BLAST. Unless you're writing a parser, you won't ever need to create a GenericHit or any other HitI-implementing object. If you use the SearchIO system, HitI objects ar...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::SearchResultEventBuilder - Event Handler for SearchIO events.
This object handles Search Events generated by the SearchIO classes and build appropriate FAST::Bio::Search::* objects from them....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing
This interface describes the basic methods needed to handle Events thrown from parsing a Search Result such as FASTA, BLAST, or HMMer....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC