Search results for "distribution:FAST CJFIELDS"
FAST::Bio::Species - Generic species object.
NOTE: This class is planned for deprecation in favor of the simpler FAST::Bio::Taxon. Please use that class instead. Provides a very simple object for storing phylogenetic information. The classification is stored in an array, which is a list of node...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::arp - ARP MSA Sequence input/output stream
This object can create FAST::Bio::SimpleAlign objects from ARP flat files. These are typically configuration-like data files for the program Arlequin. For more information, see: http://lgb.unige.ch/arlequin/ For the moment, this retains the allele se...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::HandlerBaseI - Interface class for handler methods which interact with any event-driven parsers (drivers).
This interface describes simple class methods used for processing data from an event-based parser (a driver). This is similar in theme to an XML SAX-based driver but differs in that one can optionally pass related data semi-intelligently as chunks (d...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::fastq - fastq sequence input/output stream
This object can transform FAST::Bio::Seq and FAST::Bio::Seq::Quality objects to and from FASTQ flat file databases. FASTQ is a file format used frequently at the Sanger Centre and in next-gen sequencing to bundle a FASTA sequence and its quality data...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::genbank - GenBank sequence input/output stream
This object can transform FAST::Bio::Seq objects to and from GenBank flat file databases. There is some flexibility here about how to write GenBank output that is not fully documented. Optional functions _show_dna() (output only) shows the dna or not...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::erpin - SearchIO-based ERPIN parser
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....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::infernal - SearchIO-based Infernal parser
This is a SearchIO-based parser for Infernal output from the cmsearch program. It currently parses cmsearch output for Infernal versions 0.7-1.0; older versions may work but will not be supported. As the first stable version has been released (and ou...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SearchIO::rnamotif - SearchIO-based RNAMotif parser
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...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::stockholm - stockholm sequence input/output stream
This object can transform FAST::Bio::Align::AlignI objects to and from stockholm flat file databases. This has been completely refactored from the original stockholm parser to handle annotation data and now includes a write_aln() method for (almost) ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Factory::FTLocationFactory - A FeatureTable Location Parser
Implementation of string-encoded location parsing for the Genbank feature table encoding of locations....
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::SeqIO::Handler::GenericRichSeqHandler - FAST::Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data
This is an experimental implementation of a sequence-based HandlerBaseI parser and may change over time. It is possible (nay, likely) that the way handler methods are set up will change over development to allow more flexibility. Release pumpkins, pl...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::Handler::GenericAlignHandler - FAST::Bio::HandlerI-based generic data handler class for alignment-based data
This is an experimental implementation of a alignment-based HandlerBaseI parser and may change over time. It is possible that the way handler methods are set up will change over development to allow more flexibility. Standard Developer caveats: Here ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC