Search results for "dist:BioPerl Bio::SearchIO::blast"
Bio::SearchIO::blast - Event generator for event based parsing of blast reports
This object encapsulated the necessary methods for generating events suitable for building Bio::Search objects from a BLAST report file. Read the Bio::SearchIO for more information about how to use this. This driver can parse: * NCBI produced plain t...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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 Bio::SearchIO::* - you should not need to ever use those format parsers directly. (For people used...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::BlastUtils - Utility functions for Bio::Search:: BLAST objects
The BlastUtils.pm module is a collection of subroutines used primarily by 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, and i...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Index::Blast - Indexes Blast reports and supports retrieval based on query accession(s)
This object allows one to build an index on a blast file (or files) and provide quick access to the blast report for that accession. This also allows for ID parsing using a callback: $inx->id_parser(\&get_id); # make the index $inx->make_index($file_...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::megablast - a driver module for 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'=='[...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::BlastHit - Blast-specific subclass of Bio::Search::Hit::GenericHit
This object is a subclass of Bio::Search::Hit::GenericHit and provides some operations that facilitate working with BLAST and PSI-BLAST Hits. For general information about working with Hits, see Bio::Search::Hit::GenericHit....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
bp_search2gff - turn a SearchIO report into GFF
This script will turn a SearchIO report (BLAST, FASTP, SSEARCH, AXT, WABA) into GFF. The options are: -i infilename - (optional) inputfilename, will read either ARGV files or from STDIN -o filename - the output filename [default STDOUT] -f format - s...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Index::BlastTable - Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)
This object allows one to build an index on a tabular BLAST file (or files) and provide quick access to the blast report for that accession. This also allows for ID parsing using a callback: $inx->id_parser(\&get_id); # make the index $inx->make_inde...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::SearchUtils - Utility functions for Bio::Search:: objects
The SearchUtils.pm module is a collection of subroutines used primarily by 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....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::HSP::BlastHSP - Bioperl BLAST High-Scoring Pair object
A Bio::Search::HSP::BlastHSP object provides an interface to data obtained in a single alignment section of a Blast report (known as a "High-scoring Segment Pair"). This is essentially a pairwise alignment with score information. BlastHSP objects are...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::bl2seq - bl2seq sequence input/output stream
This object can create Bio::SimpleAlign sequence alignment objects (of two sequences) from "bl2seq" BLAST reports. A nice feature of this module is that - in combination with Bio::Tools::Run::StandAloneBlast.pm or a remote BLAST - it can be used to a...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::PsiBlastHit - Bioperl BLAST Hit object
The Bio::Search::Hit::PsiBlastHit.pm module encapsulates data and methods for manipulating "hits" from a BLAST report. A BLAST hit is a collection of HSPs along with other metadata such as sequence name and score information. Hit objects are accessed...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
bp_search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocks
This script will parse and filter BLAST (or other formats Bio::SearchIO can parse) output and format the alignment as blocks of alignments based on the HSPs. Note this can only work if the input file parsed contains the necessary. Typically this can ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::gmap_f9 - Event generator for parsing gmap reports (Z format)
This object encapsulated the necessary methods for generating events suitable for building Bio::Search objects from a GMAP "compressed" report (from gmap run with -Z flag) Read the Bio::SearchIO for more information about how to use this. REVERSE STR...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::HitI - Interface for a hit in a similarity search result
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....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::PullHitI - 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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::HSP::PullHSPI - 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 Bio::PullPa...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC