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Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
---|---|---|---|---|
16 | 2 | 4 | 0.973 | stmt_list[7] |
Clone Abstraction | Parameter Bindings |
Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
---|---|---|---|
1 | 18 | 250 | Bio/AlignIO/FastaIO.py |
2 | 16 | 270 | Bio/AlignIO/FastaIO.py |
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record = alignment.get_all_seqs( )[ -1] assert record.id==self._query_descr or record.description==self._query_descr #assert record.seq.tostring() == query_align_seq record.id = self._query_descr.split(None,1)[0].strip(",") record.name = "query" record.annotations["original_length"] = int(query_annotation["sq_len"]) #TODO - What if a specific alphabet has been requested? #TODO - Use an IUPAC alphabet? #TODO - Can FASTA output RNA? if alphabet==single_letter_alphabet and "sq_type" in query_annotation: if query_annotation["sq_type"]=="D": record.seq.alphabet = generic_dna elif query_annotation["sq_type"]=="p": record.seq.alphabet = generic_protein if "-" in query_align_seq: if not hasattr(record.seq.alphabet,"gap_char"): record.seq.alphabet = Gapped(record.seq.alphabet,"-") |
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record = alignment.get_all_seqs( )[ -1] assert record.id==match_descr or record.description==match_descr #assert record.seq.tostring() == match_align_seq record.id = match_descr.split(None,1)[0].strip(",") record.name = "match" record.annotations["original_length"] = int(match_annotation["sq_len"]) #This is still a very crude way of dealing with the alphabet: if alphabet==single_letter_alphabet and "sq_type" in match_annotation: if match_annotation["sq_type"]=="D": record.seq.alphabet = generic_dna elif match_annotation["sq_type"]=="p": record.seq.alphabet = generic_protein if "-" in match_align_seq: if not hasattr(record.seq.alphabet,"gap_char"): record.seq.alphabet = Gapped(record.seq.alphabet,"-") |
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record = alignment.get_all_seqs( )[ -1] assert record.id== [[#variable2d8f83a0]]or record.description== [[#variable2d8f83a0]] #assert record.seq.tostring() == match_align_seq #assert record.seq.tostring() == query_align_seq record.id = [[#variable2d8f83a0]].split(None,1)[0].strip(",") record.name = [[#variable6aef9380]] record.annotations["original_length"] = int( [[#variable6aef8ec0]]["sq_len"]) #This is still a very crude way of dealing with the alphabet: #TODO - What if a specific alphabet has been requested? #TODO - Use an IUPAC alphabet? #TODO - Can FASTA output RNA? if alphabet==single_letter_alphabet and "sq_type" in [[#variable6aef8ec0]]: if [[#variable6aef8ec0]]["sq_type"]=="D": record.seq.alphabet = generic_dna elif [[#variable6aef8ec0]]["sq_type"]=="p": record.seq.alphabet = generic_protein if "-" in [[#variable6aef9360]]: if not hasattr(record.seq.alphabet,"gap_char"): record.seq.alphabet = Gapped(record.seq.alphabet,"-") |
CloneAbstraction |
Parameter Index | Clone Instance | Parameter Name | Value |
---|---|---|---|
1 | 1 | [[#2d8f83a0]] | match_descr |
1 | 2 | [[#2d8f83a0]] | self._query_descr |
2 | 1 | [[#6aef9380]] | "match" |
2 | 2 | [[#6aef9380]] | "query" |
3 | 1 | [[#6aef8ec0]] | match_annotation |
3 | 2 | [[#6aef8ec0]] | query_annotation |
4 | 1 | [[#6aef9360]] | match_align_seq |
4 | 2 | [[#6aef9360]] | query_align_seq |