[Biopython] How do I retrieve information regarding isolation_source and clones using Entrez

[Young Song]

Hi,

   I have spent few hours reading the Biopython manual, and I am currently
trying to write a script that can retrieve information regarding
isolation_source and clone name for certain sequences.  This is the code
that I have now:

>>from Bio import Entrez

>>Entrez.email = "youngcsong at gmail.com"
>>entrez_handle = Entrez.efetch(db="protein", id="ADJ51069", retmode="xml")
>>entrez_record = Entrez.read(entrez_handle)

>>print entrez_record[0].keys()

Then I get the following:

[u'GBSeq_moltype', u'GBSeq_source', u'GBSeq_sequence',
u'GBSeq_primary-accession', u'GBSeq_definition', u'GBSeq_accession-version',
u'GBSeq_topology', u'GBSeq_length', u'*GBSeq_feature-table*',
u'GBSeq_create-date', u'GBSeq_other-seqids', u'GBSeq_division',
u'GBSeq_taxonomy', u'GBSeq_comment', u'GBSeq_source-db',
u'GBSeq_references', u'GBSeq_update-date', u'GBSeq_organism',
u'GBSeq_locus']

I used the key, "GBSeq_feature-table" to see what sort of values are stored
here,

>>print records[0]["GBSeq_feature-table"]

Then I get following, which seems rather confusing:

[{u'GBFeature_quals': [{u'GBQualifier_name': 'organism',
u'GBQualifier_value': 'uncultured prokaryote'}, *{u'GBQualifier_name':
'isolation_source', u'GBQualifier_value': 'contaminated river sediment'}*,
{u'GBQualifier_name': 'db_xref', u'GBQualifier_value':
'taxon:198431'}, *{u'GBQualifier_name':
'clone', u'GBQualifier_value': '**Arthur_Kill_OTU4'}*, {u'GBQualifier_name':
'environmental_sample'}, {u'GBQualifier_name': 'country',
u'GBQualifier_value': 'USA: New Jersey'}], u'GBFeature_key': 'source',
u'GBFeature_intervals': [{u'GBInterval_from': '1', u'GBInterval_to': '218',
u'GBInterval_accession': 'ADJ51069.1'}], u'GBFeature_location': '1..218'},
{u'GBFeature_quals': [{u'GBQualifier_name': 'product', u'GBQualifier_value':
'alkylsuccinate synthase'}], u'GBFeature_intervals': [{u'GBInterval_from':
'1', u'GBInterval_to': '218', u'GBInterval_accession': 'ADJ51069.1'}],
u'GBFeature_location': '<1..>218', u'GBFeature_key': 'Protein',
u'GBFeature_partial5': StringElement('', attributes={u'value': u'true'}),
u'GBFeature_partial3': StringElement('', attributes={u'value': u'true'})},
{u'GBFeature_quals': [{u'GBQualifier_name': 'region_name',
u'GBQualifier_value': 'RNR_PFL'}, {u'GBQualifier_name': 'note',
u'GBQualifier_value': 'Ribonucleotide reductase and Pyruvate formate lyase;
cl09939'}, {u'GBQualifier_name': 'db_xref', u'GBQualifier_value':
'CDD:186877'}], u'GBFeature_intervals': [{u'GBInterval_from': '1',
u'GBInterval_to': '218', u'GBInterval_accession': 'ADJ51069.1'}],
u'GBFeature_location': '<1..>218', u'GBFeature_key': 'Region',
u'GBFeature_partial5': StringElement('', attributes={u'value': u'true'}),
u'GBFeature_partial3': StringElement('', attributes={u'value': u'true'})},
{u'GBFeature_quals': [{u'GBQualifier_name': 'gene', u'GBQualifier_value':
'assA'}, {u'GBQualifier_name': 'coded_by', u'GBQualifier_value':
'GU453639.1:<1..>658'}, {u'GBQualifier_name': 'codon_start',
u'GBQualifier_value': '3'}, {u'GBQualifier_name': 'transl_table',
u'GBQualifier_value': '11'}], u'GBFeature_intervals': [{u'GBInterval_from':
'1', u'GBInterval_to': '218', u'GBInterval_accession': 'ADJ51069.1'}],
u'GBFeature_location': '1..218', u'GBFeature_key': 'CDS',
u'GBFeature_partial5': StringElement('', attributes={u'value': u'true'}),
u'GBFeature_partial3': StringElement('', attributes={u'value': u'true'})}]

It seems like there is some attributes called GBQualifier_name and
GBQualifier_value, but I am not sure how to utilize these attributes to get
the bolded values (i.e. contaminated river sediment and Arthur_Kill_OTU4).
Your help here would be very much appreciated.  Thank you in advance.

Young
-- 
Young C. Song
Masters Student
Graduate Program in Bioinformatics
The University of British Columbia
Department of Microbiology and Immunology
2350 Health Science Mall
Vancouver, BC V6T 1Z4, Canada