pydna.genbank

This module provides a class for downloading sequences from genbank called Genbank and an function that does the same thing called genbank.

The function can be used if the environmental variable pydna_email has been set to a valid email address. The easiest way to do this permanantly is to edit the pydna.ini file. See the documentation of pydna.open_config_folder()

class pydna.genbank.Genbank(users_email: str, *, tool: str = 'pydna')

Bases: object

Class to facilitate download from genbank. It is easier and quicker to use the pydna.genbank.genbank() function directly.

Parameters:

users_email (string) – Has to be a valid email address. You should always tell Genbanks who you are, so that they can contact you.

Examples

>>> from pydna.genbank import Genbank
>>> gb=Genbank("bjornjobb@gmail.com")
>>> rec = gb.nucleotide("LP002422.1")   # <- entry from genbank
>>> print(len(rec))
1

nucleotide(**kwargs)

pydna.genbank.genbank(accession: str = 'CS570233.1', *args, **kwargs) → GenbankRecord

Download a genbank nuclotide record.

This function takes the same paramenters as the :func:pydna.genbank.Genbank.nucleotide method. The email address stored in the pydna_email environment variable is used. The easiest way set this permanantly is to edit the pydna.ini file. See the documentation of pydna.open_config_folder()

if no accession is given, a very short Genbank entry is used as an example (see below). This can be useful for testing the connection to Genbank.

Please note that this result is also cached by default by settings in the pydna.ini file. See the documentation of pydna.open_config_folder()

LOCUS       CS570233                  14 bp    DNA     linear   PAT 18-MAY-2007
DEFINITION  Sequence 6 from Patent WO2007025016.
ACCESSION   CS570233
VERSION     CS570233.1
KEYWORDS    .
SOURCE      synthetic construct
  ORGANISM  synthetic construct
            other sequences; artificial sequences.
REFERENCE   1
  AUTHORS   Shaw,R.W. and Cottenoir,M.
  TITLE     Inhibition of metallo-beta-lactamase by double-stranded dna
  JOURNAL   Patent: WO 2007025016-A1 6 01-MAR-2007;
            Texas Tech University System (US)
FEATURES             Location/Qualifiers
     source          1..14
                     /organism="synthetic construct"
                     /mol_type="unassigned DNA"
                     /db_xref="taxon:32630"
                     /note="This is a 14bp aptamer inhibitor."
ORIGIN
        1 atgttcctac atga
//