CloneSet68


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

Clone Instance
1

Line Count
18

Source Line
250

Source File

Bio/AlignIO/FastaIO.py

        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,"-")

Clone Instance
2

Line Count
16

Source Line
270

Source File

Bio/AlignIO/FastaIO.py

        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,"-")

Clone Abstraction

Parameter Count: 4

Parameter Bindings

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 Bindings
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