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Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
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36 | 3 | 4 | 0.983 | compound_stmt |
Clone Abstraction | Parameter Bindings |
Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
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1 | 36 | 703 | Bio/Prosite/__init__.py |
2 | 36 | 296 | Bio/Prosite/Prodoc.py |
3 | 36 | 1192 | Bio/SwissProt/SProt.py |
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def index_file(filename,indexname,rec2key = None): """index_file(filename, indexname, rec2key=None) Index a Prosite file. filename is the name of the file. indexname is the name of the dictionary. rec2key is an optional callback that takes a Record and generates a unique key (e.g. the accession number) for the record. If not specified, the id name will be used. """ import os if not os.path.exists(filename): raise ValueError("%s does not exist"%filename) index = Index.Index(indexname,truncate = 1) index[Dictionary._Dictionary__filename_key] = filename handle = open(filename) records = parse(handle) end = 0 for record in records: start = end end = long(handle.tell( )) length = end-start if rec2key is not None: key = rec2key(record) else: key = record.name if not key: raise KeyError("empty key was produced") elif key in index: raise KeyError("duplicate key %s found"%key) index[key] = start,length |
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def index_file(filename,indexname,rec2key = None): """index_file(filename, indexname, rec2key=None) Index a Prodoc file. filename is the name of the file. indexname is the name of the dictionary. rec2key is an optional callback that takes a Record and generates a unique key (e.g. the accession number) for the record. If not specified, the id name will be used. """ import os if not os.path.exists(filename): raise ValueError("%s does not exist"%filename) index = Index.Index(indexname,truncate = 1) index[Dictionary._Dictionary__filename_key] = filename handle = open(filename) records = parse(handle) end = 0 for record in records: start = end end = long(handle.tell( )) length = end-start if rec2key is not None: key = rec2key(record) else: key = record.accession if not key: raise KeyError("empty key was produced") elif key in index: raise KeyError("duplicate key %s found"%key) index[key] = start,length |
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def index_file(filename,indexname,rec2key = None): """index_file(filename, indexname, rec2key=None) Index a SwissProt file. filename is the name of the file. indexname is the name of the dictionary. rec2key is an optional callback that takes a Record and generates a unique key (e.g. the accession number) for the record. If not specified, the entry name will be used. """ from Bio.SwissProt import parse if not os.path.exists(filename): raise ValueError("%s does not exist"%filename) index = Index.Index(indexname,truncate = 1) index[Dictionary._Dictionary__filename_key] = filename handle = open(filename) records = parse(handle) end = 0 for record in records: start = end end = long(handle.tell( )) length = end-start if rec2key is not None: key = rec2key(record) else: key = record.entry_name if not key: raise KeyError("empty sequence key was produced") elif key in index: raise KeyError("duplicate key %s found"%key) index[key] = start,length |
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def index_file(filename,indexname,rec2key = None): [[#variable71a59b40]] [[#variable71a59ac0]] if not os.path.exists(filename): raise ValueError("%s does not exist"%filename) index = Index.Index(indexname,truncate = 1) index[Dictionary._Dictionary__filename_key] = filename handle = open(filename) records = parse(handle) end = 0 for record in records: start = end end = long(handle.tell( )) length = end-start if rec2key is not None: key = rec2key(record) else: key = record. [[#variable71a59a60]] if not key: raise KeyError( [[#variable71a59960]]) elif key in index: raise KeyError("duplicate key %s found"%key) index[key] = start,length |
CloneAbstraction |
Parameter Index | Clone Instance | Parameter Name | Value |
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1 | 1 | [[#71a59b40]] | """index_file(filename, indexname, rec2key=None) Index a Prodoc file. filename is the name of the file. indexname is the name of the dictionary. rec2key is an optional callback that takes a Record and generates a unique key (e.g. the accession number) for the record. If not specified, the id name will be used. """ |
1 | 2 | [[#71a59b40]] | """index_file(filename, indexname, rec2key=None) Index a Prosite file. filename is the name of the file. indexname is the name of the dictionary. rec2key is an optional callback that takes a Record and generates a unique key (e.g. the accession number) for the record. If not specified, the id name will be used. """ |
1 | 3 | [[#71a59b40]] | """index_file(filename, indexname, rec2key=None) Index a SwissProt file. filename is the name of the file. indexname is the name of the dictionary. rec2key is an optional callback that takes a Record and generates a unique key (e.g. the accession number) for the record. If not specified, the entry name will be used. """ |
2 | 1 | [[#71a59ac0]] | import os |
2 | 2 | [[#71a59ac0]] | import os |
2 | 3 | [[#71a59ac0]] | from Bio.SwissProt import parse |
3 | 1 | [[#71a59a60]] | accession |
3 | 2 | [[#71a59a60]] | name |
3 | 3 | [[#71a59a60]] | entry_name |
4 | 1 | [[#71a59960]] | "empty key was produced" |
4 | 2 | [[#71a59960]] | "empty key was produced" |
4 | 3 | [[#71a59960]] | "empty sequence key was produced" |