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# Copyright 2006-2013,2020 by Peter Cock.
# Revisions copyright 2008-2009 by Michiel de Hoon.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO support for the "swiss" (aka SwissProt/UniProt) file format.
You are expected to use this module via the Bio.SeqIO functions.
See also the Bio.SwissProt module which offers more than just accessing
the sequences as SeqRecord objects.
See also Bio.SeqIO.UniprotIO.py which supports the "uniprot-xml" format.
"""
from Bio import SeqFeature
from Bio import SwissProt
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
def SwissIterator(source):
"""Break up a Swiss-Prot/UniProt file into SeqRecord objects.
Argument source is a file-like object or a path to a file.
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.
Rather than calling it directly, you are expected to use this
parser via Bio.SeqIO.parse(..., format="swiss") instead.
"""
swiss_records = SwissProt.parse(source)
for swiss_record in swiss_records:
# Convert the SwissProt record to a SeqRecord
record = SeqRecord(
Seq(swiss_record.sequence),
id=swiss_record.accessions[0],
name=swiss_record.entry_name,
description=swiss_record.description,
features=swiss_record.features,
)
for cross_reference in swiss_record.cross_references:
if len(cross_reference) < 2:
continue
database, accession = cross_reference[:2]
dbxref = f"{database}:{accession}"
if dbxref not in record.dbxrefs:
record.dbxrefs.append(dbxref)
annotations = record.annotations
annotations["molecule_type"] = "protein"
annotations["accessions"] = swiss_record.accessions
if swiss_record.protein_existence:
annotations["protein_existence"] = swiss_record.protein_existence
if swiss_record.created:
date, version = swiss_record.created
annotations["date"] = date
annotations["sequence_version"] = version
if swiss_record.sequence_update:
date, version = swiss_record.sequence_update
annotations["date_last_sequence_update"] = date
annotations["sequence_version"] = version
if swiss_record.annotation_update:
date, version = swiss_record.annotation_update
annotations["date_last_annotation_update"] = date
annotations["entry_version"] = version
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(f"Unknown key {key} found in references")
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
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