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# Copyright 1999 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Code to parse the keywlist.txt file from SwissProt/UniProt
See:
http://www.expasy.ch/sprot/sprot-top.html
ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/keywlist.txt
Classes:
- Record Stores the information about one keyword or one category
in the keywlist.txt file.
Functions:
- parse Parses the keywlist.txt file and returns an iterator to
the records it contains.
"""
from __future__ import print_function
class Record(dict):
"""
This record stores the information of one keyword or category in the
keywlist.txt as a Python dictionary. The keys in this dictionary are
the line codes that can appear in the keywlist.txt file::
--------- --------------------------- ----------------------
Line code Content Occurrence in an entry
--------- --------------------------- ----------------------
ID Identifier (keyword) Once; starts a keyword entry
IC Identifier (category) Once; starts a category entry
AC Accession (KW-xxxx) Once
DE Definition Once or more
SY Synonyms Optional; once or more
GO Gene ontology (GO) mapping Optional; once or more
HI Hierarchy Optional; once or more
WW Relevant WWW site Optional; once or more
CA Category Once per keyword entry; absent
in category entries
"""
def __init__(self):
dict.__init__(self)
for keyword in ("DE", "SY", "GO", "HI", "WW"):
self[keyword] = []
def parse(handle):
record = Record()
# First, skip the header - look for start of a record
for line in handle:
if line.startswith("ID "):
# Looks like there was no header
record["ID"] = line[5:].strip()
break
if line.startswith("IC "):
# Looks like there was no header
record["IC"] = line[5:].strip()
break
# Now parse the records
for line in handle:
if line.startswith("-------------------------------------"):
# We have reached the footer
break
key = line[:2]
if key == "//":
record["DE"] = " ".join(record["DE"])
record["SY"] = " ".join(record["SY"])
yield record
record = Record()
elif line[2:5] == " ":
value = line[5:].strip()
if key in ("ID", "IC", "AC", "CA"):
record[key] = value
elif key in ("DE", "SY", "GO", "HI", "WW"):
record[key].append(value)
else:
print("Ignoring: %s" % line.strip())
# Read the footer and throw it away
for line in handle:
pass
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