Package Bio :: Package SwissProt :: Module KeyWList
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Source Code for Module Bio.SwissProt.KeyWList

 1  # Copyright 1999 by Jeffrey Chang.  All rights reserved. 
 2  # This code is part of the Biopython distribution and governed by its 
 3  # license.  Please see the LICENSE file that should have been included 
 4  # as part of this package. 
 5   
 6  """Code to parse the keywlist.txt file from SwissProt/UniProt 
 7   
 8  See: 
 9  http://www.expasy.ch/sprot/sprot-top.html 
10  ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/keywlist.txt 
11   
12  Classes: 
13  Record            Stores the information about one keyword or one category 
14                    in the keywlist.txt file. 
15   
16  Functions: 
17  parse             Parses the keywlist.txt file and returns an iterator to 
18                    the records it contains. 
19  """ 
20   
21   
22 -class Record(dict):
23 """ 24 This record stores the information of one keyword or category in the 25 keywlist.txt as a Python dictionary. The keys in this dictionary are 26 the line codes that can appear in the keywlist.txt file: 27 28 --------- --------------------------- ---------------------- 29 Line code Content Occurrence in an entry 30 --------- --------------------------- ---------------------- 31 ID Identifier (keyword) Once; starts a keyword entry 32 IC Identifier (category) Once; starts a category entry 33 AC Accession (KW-xxxx) Once 34 DE Definition Once or more 35 SY Synonyms Optional; once or more 36 GO Gene ontology (GO) mapping Optional; once or more 37 HI Hierarchy Optional; once or more 38 WW Relevant WWW site Optional; once or more 39 CA Category Once per keyword entry; absent 40 in category entries 41 """
42 - def __init__(self):
43 dict.__init__(self) 44 for keyword in ("DE", "SY", "GO", "HI", "WW"): 45 self[keyword] = []
46
47 -def parse(handle):
48 record = Record() 49 # First, skip the header - look for start of a record 50 for line in handle: 51 if line.startswith("ID "): 52 # Looks like there was no header 53 record["ID"] = line[5:].strip() 54 break 55 if line.startswith("IC "): 56 # Looks like there was no header 57 record["IC"] = line[5:].strip() 58 break 59 # Now parse the records 60 for line in handle: 61 if line.startswith("-------------------------------------"): 62 # We have reached the footer 63 break 64 key = line[:2] 65 if key=="//": 66 record["DE"] = " ".join(record["DE"]) 67 record["SY"] = " ".join(record["SY"]) 68 yield record 69 record = Record() 70 elif line[2:5]==" ": 71 value = line[5:].strip() 72 if key in ("ID", "IC", "AC", "CA"): 73 record[key] = value 74 elif key in ("DE", "SY", "GO", "HI", "WW"): 75 record[key].append(value) 76 else: 77 print "Ignoring: %s" % line.strip() 78 # Read the footer and throw it away 79 for line in handle: 80 pass
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