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Merge pull request #8 from abretaud/typedefs
Properly load orphan typedefs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,142 @@ | ||
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| #!/usr/bin/env python | ||
| # -*- coding: utf-8 -*- | ||
| """ | ||
| A parser for the OBO v1.2 format | ||
| Inspired from https://techoverflow.net/blog/2013/11/18/a-geneontology-obo-v1.2-parser-in-python/ | ||
| """ | ||
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| from __future__ import with_statement, print_function | ||
| from collections import OrderedDict | ||
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| __author__ = "Uli Koehler, Anthony Bretaudeau" | ||
| __copyright__ = "Copyright 2013 Uli Koehler, 2016 Anthony Bretaudeau" | ||
| __license__ = "Apache v2.0" | ||
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| def processTerm(term): | ||
| """ | ||
| In an object representing a term, replace single-element lists with | ||
| their only member. | ||
| Returns the modified object as a dictionary. | ||
| """ | ||
| ret = term #Input is a OrderedDict, might express unexpected behaviour | ||
| for key, value in ret.iteritems(): | ||
| if len(value) == 1: | ||
| ret[key] = value[0] | ||
| return ret | ||
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| def parseHeader(filename): | ||
| """ | ||
| Parses a file in OBO v1.2 format. | ||
| Yields each term | ||
| Keyword arguments: | ||
| filename: The filename to read | ||
| """ | ||
| header = "" | ||
| with open(filename, "r") as infile: | ||
| currentTerm = None | ||
| for line in infile: | ||
| line = line.strip() | ||
| if not line: continue #Skip empty | ||
| if line == "[Term]" or line == "[Typedef]": | ||
| return header | ||
| else: #Not [Term] | ||
| header += line + "\n" | ||
| return header | ||
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| def parseOBOTerms(filename): | ||
| """ | ||
| Parses a file in OBO v1.2 format. | ||
| Yields each term | ||
| Keyword arguments: | ||
| filename: The filename to read | ||
| """ | ||
| with open(filename, "r") as infile: | ||
| currentTerm = None | ||
| for line in infile: | ||
| line = line.strip() | ||
| if not line: continue #Skip empty | ||
| if line == "[Term]": | ||
| if currentTerm: yield processTerm(currentTerm) | ||
| currentTerm = OrderedDict() | ||
| elif line == "[Typedef]": | ||
| #Skip [Typedef sections] | ||
| currentTerm = None | ||
| else: #Not [Term] | ||
| #Only process if we're inside a [Term] environment | ||
| if currentTerm is None: continue | ||
| key, sep, val = line.partition(":") | ||
| if key not in currentTerm: | ||
| currentTerm[key] = [] | ||
| currentTerm[key].append(val.strip()) | ||
| #Add last term | ||
| if currentTerm is not None: | ||
| yield processTerm(currentTerm) | ||
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| def parseOBOTypedefs(filename): | ||
| """ | ||
| Parses a file in OBO v1.2 format. | ||
| Yields each typedef | ||
| Keyword arguments: | ||
| filename: The filename to read | ||
| """ | ||
| with open(filename, "r") as infile: | ||
| currentTypedef = None | ||
| for line in infile: | ||
| line = line.strip() | ||
| if not line: continue #Skip empty | ||
| if line == "[Term]": | ||
| #Skip [Term sections] | ||
| currentTypedef = None | ||
| elif line == "[Typedef]": | ||
| if currentTypedef: yield processTerm(currentTypedef) | ||
| currentTypedef = OrderedDict() | ||
| else: #Not [Term] | ||
| #Only process if we're inside a [Term] environment | ||
| if currentTypedef is None: continue | ||
| key, sep, val = line.partition(":") | ||
| if key != 'is_a': # This is not really used and causes problem with SO | ||
| if key not in currentTypedef: | ||
| currentTypedef[key] = [] | ||
| currentTypedef[key].append(val.strip()) | ||
| #Add last typedef | ||
| if currentTypedef is not None: | ||
| yield processTerm(currentTypedef) | ||
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| if __name__ == "__main__": | ||
| import argparse | ||
| parser = argparse.ArgumentParser() | ||
| parser.add_argument('infile', help='The input file in OBO v1.2 format.') | ||
| parser.add_argument('outfile', help='The output file in OBO v1.2 format with only Typedef not used in the OBO file.') | ||
| args = parser.parse_args() | ||
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| #Iterate over terms | ||
| termCounter = 0 | ||
| seenRelationships = [] | ||
| for term in parseOBOTerms(args.infile): | ||
| if 'relationship' in term: | ||
| if isinstance(term['relationship'], basestring): | ||
| seenRelationships.append(term['relationship'].split()[0]) | ||
| else: | ||
| for r in term['relationship']: | ||
| seenRelationships.append(r.split()[0]) | ||
| termCounter += 1 | ||
| print("Found %d terms" % termCounter) | ||
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| typedefCounter = 0 | ||
| unusedCounter = 0 | ||
| with open(args.outfile, "w") as outfile: | ||
| header = parseHeader(args.infile) | ||
| print(header, file=outfile) | ||
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| for typedef in parseOBOTypedefs(args.infile): | ||
| if typedef['id'] not in seenRelationships: | ||
| print("%s typedef was never seen" % typedef['name']) | ||
| print("[Typedef]", file=outfile) | ||
| for k in typedef: | ||
| print("%s: %s" % (k, typedef[k]), file=outfile) | ||
| print("", file=outfile) | ||
| unusedCounter += 1 | ||
| typedefCounter += 1 | ||
| print("Found %d typedefs, %s unused" % (typedefCounter, unusedCounter)) |
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Oh dear... didn't mean for you to have to write so much code for this problem...
Remind me to buy you a couple beverages of your choice at next gcc / food / something. Really appreciate you working on this.