CloneSet271


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Clone
Mass
Clones in
CloneSet
Parameter
Count
Clone
Similarity
Syntax Category
[Sequence Length]
29220.989stmt_list[5]
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
123140
Bio/AlignIO/NexusIO.py
229163
Bio/AlignIO/NexusIO.py
Clone Instance
1
Line Count
23
Source Line
140
Source File
Bio/AlignIO/NexusIO.py

    handle = StringIO('''#NEXUS
    [TITLE: NoName]

    begin data;
    dimensions ntax=4 nchar=50;
    format interleave datatype=protein   gap=- symbols="FSTNKEYVQMCLAWPHDRIG";

    matrix
    CYS1_DICDI          -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---- 
    ALEU_HORVU          MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG 
    CATH_HUMAN          ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK----
    CYS1_DICDI          -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---X
    ;
    end; 
    '''              ) 
    for a in NexusIterator(handle): 
        print a 
        for r in a: 
            print repr(r.seq),r.name,r.id 
        
    print "Done" 
    print 
    print "Repeated names with a TAXA block" 


Clone Instance
2
Line Count
29
Source Line
163
Source File
Bio/AlignIO/NexusIO.py

    handle = StringIO('''#NEXUS
    [TITLE: NoName]

    begin taxa
    CYS1_DICDI
    ALEU_HORVU
    CATH_HUMAN
    CYS1_DICDI;
    end;

    begin data;
    dimensions ntax=4 nchar=50;
    format interleave datatype=protein   gap=- symbols="FSTNKEYVQMCLAWPHDRIG";

    matrix
    CYS1_DICDI          -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---- 
    ALEU_HORVU          MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG 
    CATH_HUMAN          ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK----
    CYS1_DICDI          -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---X
    ;
    end; 
    '''              ) 
    for a in NexusIterator(handle): 
        print a 
        for r in a: 
            print repr(r.seq),r.name,r.id 
        
    print "Done" 
    print 
    print "Reading an empty file" 


Clone AbstractionParameter Count: 2Parameter Bindings

handle = StringIO( [[#variable76c7a7c0]]) 
for a in NexusIterator(handle):
  print a 
  for r in a:
  
    print repr(r.seq),r.name,r.id 
  
print "Done" 
print 
print [[#variable601862c0]]
 

CloneAbstraction
Parameter Bindings
Parameter
Index
Clone
Instance
Parameter
Name
Value
11[[#76c7a7c0]]
'''#NEXUS
    [TITLE: NoName]

    begin taxa
    CYS1_DICDI
    ALEU_HORVU
    CATH_HUMAN
    CYS1_DICDI;
    end;

    begin data;
    dimensions ntax=4 nchar=50;
    format interleave datatype=protein   gap=- symbols="FSTNKEYVQMCLAWPHDRIG";

    matrix
    CYS1_DICDI          -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---- 
    ALEU_HORVU          MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG 
    CATH_HUMAN          ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK----
    CYS1_DICDI          -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---X
    ;
    end; 
    ''' 
12[[#76c7a7c0]]
'''#NEXUS
    [TITLE: NoName]

    begin data;
    dimensions ntax=4 nchar=50;
    format interleave datatype=protein   gap=- symbols="FSTNKEYVQMCLAWPHDRIG";

    matrix
    CYS1_DICDI          -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---- 
    ALEU_HORVU          MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG 
    CATH_HUMAN          ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK----
    CYS1_DICDI          -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---X
    ;
    end; 
    ''' 
21[[#601862c0]]
"Reading an empty file" 
22[[#601862c0]]
"Repeated names with a TAXA block"