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Merge pull request #288 from OBOFoundry/revised
COB Revised -- Wait for James to Merge
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| Ontology ID Label Type Definition Deprecated Term Replaced By | ||
| ID LABEL TYPE A IAO:0000115 AT owl:deprecated^^xsd:boolean AI IAO:0100001 | ||
| COB:0000005 obsolete elementary charge owl:Class true | ||
| COB:0000014 obsolete macromolecular entity owl:Class true | ||
| COB:0000020 obsolete subcellular structure owl:Class true GO:0110165 | ||
| COB:0000032 obsolete geographical location owl:Class true | ||
| COB:0000056 obsolete immaterial anatomical entity owl:Class true UBERON:0000466 | ||
| COB:0000073 obsolete gene product owl:Class true | ||
| COB:0000077 obsolete action specification owl:Class true IAO:0000007 | ||
| COB:0000116 obsolete cellular membrane owl:Class true | ||
| COB:0000122 obsolete physical information carrier owl:Class true |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,98 @@ | ||
| #!/usr/bin/env python3 | ||
| # | ||
| # Split the cob-edit.tsv file into three ROBOT templates: | ||
| # cob-base.tsv cob-full.tsv cob-root.tsv | ||
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| import argparse | ||
| import csv | ||
| import os | ||
| import re | ||
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| def initialize_tsv(output_dir, filename, fieldnames, robot_row): | ||
| '''Initialize and return a DictWriter for a ROBOT template.''' | ||
| path = os.path.join(output_dir, filename) | ||
| path_fh = open(path, 'w') | ||
| writer = csv.DictWriter(path_fh, fieldnames, delimiter='\t', lineterminator='\n', extrasaction='ignore') | ||
| writer.writeheader() | ||
| writer.writerow(robot_row) | ||
| return writer | ||
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| def split(input_path, output_dir): | ||
| '''Split the COB term template into base, full, and root templates.''' | ||
| header_row = None | ||
| robot_row, terms, replacements = {}, {}, {} | ||
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| with open(input_path) as f: | ||
| rows = csv.DictReader(f, delimiter='\t') | ||
| for row in rows: | ||
| if not header_row: | ||
| header_row = list(row.keys()) | ||
| id = row['Ontology ID'].strip() | ||
| if id == '': | ||
| continue | ||
| if id == 'ID': | ||
| robot_row = row | ||
| continue | ||
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| # Handle the Replacement columns | ||
| # by collecting a dictionary of replacements. | ||
| replacement_id = row['Replacement ID'].strip() | ||
| replacement_label = row['Replacement Label'].strip() | ||
| if replacement_label and replacement_label != '': | ||
| # removed exception for non-base IDs... TBD if needed/wanted | ||
| replacements[row['Label'].strip()] = { | ||
| 'ID': id, | ||
| 'Replacement Label': replacement_label, | ||
| 'Replacement ID': replacement_id, | ||
| } | ||
| # Otherwise just add this row to 'terms'. | ||
| else: | ||
| terms[id] = row | ||
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| ignore = [ | ||
| 'COB Module', 'COB Module Reason', | ||
| 'Replacement ID', 'Replacement Label', | ||
| 'Comment' | ||
| ] | ||
| fieldnames = [x for x in header_row if x not in ignore] | ||
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| # Apply replacements to the axioms in all the logical columns | ||
| axiom_cols = [ | ||
| 'Parent Class', 'Subclass Axiom', 'Equivalent Class Axiom', | ||
| 'Disjoint Class', 'Parent Property', 'Domain', 'Range', | ||
| 'Inverse Property' | ||
| ] | ||
| for id, row in terms.items(): | ||
| for repl_label, repl_dict in replacements.items(): | ||
| for col in axiom_cols: | ||
| if col not in row: | ||
| continue | ||
| row[col] = re.sub(repl_label, repl_dict['Replacement Label'], row[col]) | ||
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| base_writer = initialize_tsv(output_dir, 'cob-base.tsv', fieldnames, robot_row) | ||
| full_writer = initialize_tsv(output_dir, 'cob-full.tsv', fieldnames, robot_row) | ||
| root_writer = initialize_tsv(output_dir, 'cob-root.tsv', fieldnames, robot_row) | ||
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| for id, row in terms.items(): | ||
| module = row['COB Module'].strip() | ||
| if module == 'BASE': | ||
| base_writer.writerow(row) | ||
| if module not in ['', 'ROOT']: | ||
| full_writer.writerow(row) | ||
| if module != '': | ||
| root_writer.writerow(row) | ||
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| def main(): | ||
| parser = argparse.ArgumentParser(description='Split the main COB term template into multiple module templates') | ||
| parser.add_argument('input', type=str, help='The input COB term template') | ||
| parser.add_argument('outdir', type=str, help='The output directory') | ||
| args = parser.parse_args() | ||
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| split(args.input, args.outdir) | ||
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| if __name__ == '__main__': | ||
| main() |