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Represents a namespace (sub-database) within the BioSQL database.
i.e. One row in the biodatabase table, and all all rows in the bioentry table associated with it.
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Gets a DBSeqRecord object by its name Example: seq_rec = db.get_Seq_by_id('ROA1_HUMAN') The name of this method is misleading since it returns a DBSeqRecord rather than a DBSeq ojbect, and presumably was to mirror BioPerl. |
Gets a DBSeqRecord object by accession number Example: seq_rec = db.get_Seq_by_acc('X77802') The name of this method is misleading since it returns a DBSeqRecord rather than a DBSeq ojbect, and presumably was to mirror BioPerl. |
Gets a DBSeqRecord object by version number Example: seq_rec = db.get_Seq_by_ver('X77802.1') The name of this method is misleading since it returns a DBSeqRecord rather than a DBSeq ojbect, and presumably was to mirror BioPerl. |
Gets a list of DBSeqRecord objects by accession number Example: seq_recs = db.get_Seq_by_acc('X77802') The name of this method is misleading since it returns a list of DBSeqRecord objects rather than a list of DBSeq ojbects, and presumably was to mirror BioPerl. |
All the primary_ids of the sequences in the database (OBSOLETE). These maybe ids (display style) or accession numbers or something else completely different - they *are not* meaningful outside of this database implementation. Please use .keys() instead of .get_all_primary_ids() |
Get a DBSeqRecord by the primary (internal) id (OBSOLETE). Rather than db.get_Seq_by_primary_id(my_id) use db[my_id] The name of this method is misleading since it returns a DBSeqRecord rather than a DBSeq ojbect, and presumably was to mirror BioPerl. |
Load a set of SeqRecords into the BioSQL database. record_iterator is either a list of SeqRecord objects, or an Iterator object that returns SeqRecord objects (such as the output from the Bio.SeqIO.parse() function), which will be used to populate the database. fetch_NCBI_taxonomy is boolean flag allowing or preventing connection to the taxonomic database on the NCBI server (via Bio.Entrez) to fetch a detailed taxonomy for each SeqRecord. Example: from Bio import SeqIO count = db.load(SeqIO.parse(open(filename), format)) Returns the number of records loaded. |
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