Search results for "dist:BioPerl SDBM_File"
bp_index.pl - indexes files for use by bp_fetch.pl
bp_index.pl builds a bioperl index for the sequence files given in the argument list, under the index name. For example bp_index.pl nrdb /data/nrdb/nrdb.fasta would build an index called 'nrdb' as the index name for the file nrdb.fasta, and bp_index....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
bp_fetch.pl - fetches sequences from bioperl indexed databases
Fetches sequences using the DB access systems in Bioperl. The most common use of this is to bp_fetch sequences from bioperl indices built using bpindex.pl, or to fetch sequences from the NCBI website The format for retrieving sequences is delibrately...
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::Index::Abstract - Abstract interface for indexing a flat file
This object provides the basic mechanism to associate positions in files with names. The position and filenames are stored in DBM which can then be accessed later on. It is the equivalent of flat file indexing (eg, SRS or efetch). This object is the ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::IndexedBase - Base class for modules using indexed sequence files
Bio::DB::IndexedBase provides a base class for modules that want to index and read sequence files and provides persistent, random access to each sequence entry, without bringing the entire file into memory. This module is compliant with the Bio::SeqI...
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