Parsing Swissprot With Biopython

Question

[Stephen]

How can I parse the gene name from the SwissProt file "uniprot_sprot.dat" ?

I use the following code to parse the accessions:

from Bio import SwissProt
for record in SwissProt.parse(open("uniprot_sprot.dat")):
    for i in record.accessions:
         print i

That would print all the accession numbers. I also want the gene name

How do I access the other objects under record such as gene name? I tried gene_name but that doesn't seem to work. There doesn't seem to be a UML diagram in the Biopython tutorial for SwissProt parser like the BLAST parser....

[Peter]

(I tagged this with 'Biopython' as well)

Answer 1

[Andrzej Zielezinski]

The gene_name attribute of the SwissProt Record object in BioPython works absolutely fine as follows:

from Bio import SwissProt
for record in SwissProt.parse(open("uniprot_sprot.dat")):
    print record.gene_name

Here is a list of other attribute names that hold SwissProt data. I copied it from the docstring of the SwissProt module.

Holds information from a SwissProt record.

Members:
entry_name        Name of this entry, e.g. RL1_ECOLI.
data_class        Either 'STANDARD' or 'PRELIMINARY'.
molecule_type     Type of molecule, 'PRT',
sequence_length   Number of residues.

accessions        List of the accession numbers, e.g. ['P00321']
created           A tuple of (date, release).
sequence_update   A tuple of (date, release).
annotation_update A tuple of (date, release).

description       Free-format description.
gene_name         Gene name.  See userman.txt for description.
organism          The source of the sequence.
organelle         The origin of the sequence.
organism_classification  The taxonomy classification.  List of strings.
                         (http://www.ncbi.nlm.nih.gov/Taxonomy/)
taxonomy_id       A list of NCBI taxonomy id's.
host_organism     A list of names of the hosts of a virus, if any.
host_taxonomy_id  A list of NCBI taxonomy id's of the hosts, if any.
references        List of Reference objects.
comments          List of strings.
cross_references  List of tuples (db, id1[, id2][, id3]).  See the docs.
keywords          List of the keywords.
features          List of tuples (key name, from, to, description).
                  from and to can be either integers for the residue
                  numbers, '<', '>', or '?'

seqinfo           tuple of (length, molecular weight, CRC32 value)
sequence          The sequence.

[Peter]

With any python object at the python prompt try dir(pythonobject) which gives you a list of all the attributes etc. Also try help(pythonobject) which would give you the API docstrings also available here in this case: http://biopython.org/DIST/docs/api/Bio.SwissProt.Record-class.html

[Stephen]

Thank you for this helpful hint!

Answer 2

[Stephen]

Thank you for your helpful answer!