def _parse_reference(element):
reference = SeqFeature.Reference()
authors = []
scopes = []
tissues = []
journal_name = ''
pub_type = ''
pub_date = ''
for ref_element in element:
if ref_element.tag == NS + 'citation':
pub_type = ref_element.attrib['type']
if pub_type == 'submission':
pub_type += ' to the ' + ref_element.attrib['db']
if 'name' in ref_element.attrib:
journal_name = ref_element.attrib['name']
pub_date = ref_element.attrib.get('date', '')
j_volume = ref_element.attrib.get('volume', '')
j_first = ref_element.attrib.get('first', '')
j_last = ref_element.attrib.get('last', '')
for cit_element in ref_element:
if cit_element.tag == NS + 'title':
reference.title = cit_element.text
elif cit_element.tag == NS + 'authorList':
for person_element in cit_element:
authors.append(person_element.attrib['name'])
elif cit_element.tag == NS + 'dbReference':
self.ParsedSeqRecord.dbxrefs.append(cit_element.attrib['type']
+ ':' + cit_element.attrib['id'])
if cit_element.attrib['type'] == 'PubMed':
reference.pubmed_id = cit_element.attrib['id']
elif ref_element.attrib['type'] == 'MEDLINE':
reference.medline_id = cit_element.attrib['id']
elif ref_element.tag == NS + 'scope':
scopes.append(ref_element.text)
elif ref_element.tag == NS + 'source':
for source_element in ref_element:
if source_element.tag == NS + 'tissue':
tissues.append(source_element.text)
if scopes:
scopes_str = 'Scope: ' + ', '.join(scopes)
else:
scopes_str = ''
if tissues:
tissues_str = 'Tissue: ' + ', '.join(tissues)
else:
tissues_str = ''
# locations cannot be parsed since they are actually written in
# free text inside scopes so all the references are put in the
# annotation.
reference.location = []
reference.authors = ', '.join(authors)
if journal_name:
if pub_date and j_volume and j_first and j_last:
reference.journal = REFERENCE_JOURNAL % dict(name=journal_name,
volume=j_volume, first=j_first, last=j_last, pub_date=pub_date)
else:
reference.journal = journal_name
reference.comment = ' | '.join((pub_type, pub_date, scopes_str, tissues_str))
append_to_annotations('references', reference)
def SwissIterator(handle):
"""Breaks up a Swiss-Prot/UniProt file into SeqRecord objects.
Every section from the ID line to the terminating // becomes
a single SeqRecord with associated annotation and features.
This parser is for the flat file "swiss" format as used by:
* Swiss-Prot aka SwissProt
* TrEMBL
* UniProtKB aka UniProt Knowledgebase
For consistency with BioPerl and EMBOSS we call this the "swiss"
format. See also the SeqIO support for "uniprot-xml" format.
"""
swiss_records = SwissProt.parse(handle)
for swiss_record in swiss_records:
# Convert the SwissProt record to a SeqRecord
seq = Seq.Seq(swiss_record.sequence, Alphabet.generic_protein)
record = SeqRecord.SeqRecord(
seq,
id=swiss_record.accessions[0],
name=swiss_record.entry_name,
description=swiss_record.description,
features=[_make_seqfeature(*f) for f in swiss_record.features],
)
record.description = swiss_record.description
for cross_reference in swiss_record.cross_references:
if len(cross_reference) < 2:
continue
database, accession = cross_reference[:2]
dbxref = "%s:%s" % (database, accession)
if not dbxref in record.dbxrefs:
record.dbxrefs.append(dbxref)
annotations = record.annotations
annotations['accessions'] = swiss_record.accessions
if swiss_record.created:
annotations['date'] = swiss_record.created[0]
if swiss_record.sequence_update:
annotations[
'date_last_sequence_update'] = swiss_record.sequence_update[0]
if swiss_record.annotation_update:
annotations[
'date_last_annotation_update'] = swiss_record.annotation_update[
0]
if swiss_record.gene_name:
annotations['gene_name'] = swiss_record.gene_name
annotations['organism'] = swiss_record.organism.rstrip(".")
annotations['taxonomy'] = swiss_record.organism_classification
annotations['ncbi_taxid'] = swiss_record.taxonomy_id
if swiss_record.host_organism:
annotations['organism_host'] = swiss_record.host_organism
if swiss_record.host_taxonomy_id:
annotations['host_ncbi_taxid'] = swiss_record.host_taxonomy_id
if swiss_record.comments:
annotations['comment'] = "\n".join(swiss_record.comments)
if swiss_record.references:
annotations['references'] = []
for reference in swiss_record.references:
feature = SeqFeature.Reference()
feature.comment = " ".join("%s=%s;" % k_v
for k_v in reference.comments)
for key, value in reference.references:
if key == 'PubMed':
feature.pubmed_id = value
elif key == 'MEDLINE':
feature.medline_id = value
elif key == 'DOI':
pass
elif key == 'AGRICOLA':
pass
else:
raise ValueError("Unknown key %s found in references" %
key)
feature.authors = reference.authors
feature.title = reference.title
feature.journal = reference.location
annotations['references'].append(feature)
if swiss_record.keywords:
record.annotations['keywords'] = swiss_record.keywords
yield record