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Search results for "module:SearchIO"

Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...) River stage two • 60 direct dependents • 65 total dependents
33 ++

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::SearchIO::axt - a parser for axt format reports River stage two • 60 direct dependents • 65 total dependents
33 ++

This is a parser and event-generator for AXT format reports. BLASTZ reports (Schwartz et al,(2003) Genome Research, 13:103-107) are normally in LAV format but are commonly post-processed to AXT format; many precomputed BLASTZ reports, such as those f...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::SearchIO::psl - A parser for PSL output (UCSC) River stage two • 60 direct dependents • 65 total dependents
33 ++

This is a SearchIO driver for PSL format. PSL format is documented here: http://genome.ucsc.edu/goldenPath/help/customTrack.html#PSL By default it assumes PSL output came from BLAT you can override that by specifying -program_name => 'BLASTZ' when in...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::SearchIO::sim4 - parser for Sim4 alignments River stage two • 60 direct dependents • 65 total dependents
33 ++

This is a driver for the SearchIO system for parsing Sim4. http://globin.cse.psu.edu/html/docs/sim4.html Cannot parse LAV or 'exon file' formats (A=2 or A=5)...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::SearchIO::wise - Parsing of wise output as alignments River stage two • 60 direct dependents • 65 total dependents
33 ++

This object parsers Wise output using Bio::Tools::Genewise or Bio::Tools::Genomewise as a helper....

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

FAST::Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...) River stage zero No dependents
3 ++

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

Bio::SearchIO::waba - SearchIO parser for Jim Kent WABA program alignment output River stage two • 60 direct dependents • 65 total dependents
33 ++

This parser will process the waba output (NOT the human readable format)....

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::SearchIO::hmmer - A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) River stage zero No dependents
++

This object implements a parser for HMMER output. It works with both HMMER2 and HMMER3...

CJFIELDS/Bio-SearchIO-hmmer-1.7.3 - 25 Sep 2018 00:26:52 UTC

Bio::SearchIO::fasta - A SearchIO parser for FASTA results River stage two • 60 direct dependents • 65 total dependents
33 ++

This object contains the event based parsing code for FASTA format reports. It creates Bio::Search::HSP::FastaHSP objects instead of Bio::Search::HSP::GenericHSP for the HSP objects. This module will parse -m 9 -d 0 output as well as default m 1 outp...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::SearchIO::erpin - SearchIO-based ERPIN parser River stage two • 60 direct dependents • 65 total dependents
33 ++

This is an experimental SearchIO-based parser for output from the erpin program. It currently parses erpin output for ERPIN versions 4.2.5 and above; older versions may work but will not be supported....

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::SearchIO::blast - Event generator for event based parsing of blast reports River stage two • 60 direct dependents • 65 total dependents
33 ++

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::hmmer2 - A parser for HMMER output (hmmpfam, hmmsearch) River stage zero No dependents
++

This object implements a parser for HMMER output....

CJFIELDS/Bio-SearchIO-hmmer-1.7.3 - 25 Sep 2018 00:26:52 UTC

Bio::SearchIO::hmmer3 River stage zero No dependents
++

Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with both version 2 and version 3 of the HMMER package from <http://hmmer.org>....

CJFIELDS/Bio-SearchIO-hmmer-1.7.3 - 25 Sep 2018 00:26:52 UTC

Bio::SearchIO::gmap_f9 - Event generator for parsing gmap reports (Z format) River stage two • 60 direct dependents • 65 total dependents
33 ++

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::SearchIO::infernal - SearchIO-based Infernal parser River stage two • 60 direct dependents • 65 total dependents
33 ++

This is a SearchIO-based parser for Infernal output from the cmsearch program. It currently parses cmsearch output for Infernal versions 0.7-1.1; older versions may work but will not be supported. The latest version of Infernal is 1.1. The output has...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing. River stage zero No dependents
++

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...

CJFIELDS/Bio-SearchIO-blastxml-1.70 - 04 Jan 2018 02:12:33 UTC

Bio::SearchIO::rnamotif - SearchIO-based RNAMotif parser River stage two • 60 direct dependents • 65 total dependents
33 ++

This is a highly experimental SearchIO-based parser for output from the rnamotif program (one of the programs in the RNAMotif suite). It currently parses only raw rnamotif output for RNAMotif versions 3.0 and above; older versions may work but will n...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

FAST::Bio::SearchIO::axt - a parser for axt format reports River stage zero No dependents
3 ++

This is a parser and event-generator for AXT format reports. BLASTZ reports (Schwartz et al,(2003) Genome Research, 13:103-107) are normally in LAV format but are commonly post-processed to AXT format; many precomputed BLASTZ reports, such as those f...

DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC

Bio::SearchIO::megablast - a driver module for Bio::SearchIO to parse megablast reports (format 0) River stage two • 60 direct dependents • 65 total dependents
33 ++

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::SearchIO::exonerate - parser for Exonerate River stage two • 60 direct dependents • 65 total dependents
33 ++

This is a driver for the SearchIO system for parsing Exonerate (Guy Slater) output. You can get Exonerate at http://www.ebi.ac.uk/~guy/exonerate/ [until Guy puts up a Web reference,publication for it.]). An optional parameter -min_intron is supported...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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