Search results for "dist:BioPerl Bio::SeqIO::swiss"
Bio::SeqIO::swiss - Swissprot sequence input/output stream
This object can transform Bio::Seq objects to and from Swiss-Pprot flat file databases. There is a lot of flexibility here about how to dump things which needs to be documented. GN (Gene name) line management details A Uniprot/Swiss-Prot entry holds ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO - Handler for SeqIO Formats
Bio::SeqIO is a handler module for the formats in the SeqIO set (eg, Bio::SeqIO::fasta). It is the officially sanctioned way of getting at the format objects, which most people should use. The Bio::SeqIO system can be thought of like biological file ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq - Sequence object, with features
A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently Bio::Prim...
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
bp_genbank2gff3.pl - Genbank-gtgbrowse-friendly GFF3
This script uses Bio::SeqFeature::Tools::Unflattener and Bio::Tools::GFF to convert GenBank flatfiles to GFF3 with gene containment hierarchies mapped for optimal display in gbrowse. The input files are assumed to be gzipped GenBank flatfiles for ref...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::FTHelper - Helper class for EMBL/Genbank feature tables
Represents one particular Feature with the following fields key - the key of the feature loc - the location string of the feature <other fields> - other fields...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::swissdriver - SwissProt/UniProt handler-based push parser
This object can transform Bio::Seq objects to and from UniProt flat file databases. The key difference between this parser and the tried-and-true Bio::SeqIO::swiss parser is this version separates the parsing and data manipulation into a 'driver' met...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::GuessSeqFormat - Module for determining the sequence format of the contents of a file, a string, or through a filehandle.
Bio::Tools::GuessSeqFormat tries to guess the format ("swiss", "pir", "fasta" etc.) of the sequence or MSA in a file, in a scalar, or through a filehandle. The guess() method of a Bio::Tools::GuessSeqFormat object will examine the data, line by line,...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC