CloneSet271


Clone Mass	Clones in CloneSet	Parameter Count	Clone Similarity	Syntax Category [Sequence Length]
29	2	2	0.989	stmt_list[5]

Clone Abstraction

Parameter Bindings

Clone Instance (Click to see clone)	Line Count	Source Line	Source File
1	23	140	Bio/AlignIO/NexusIO.py
2	29	163	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 Abstraction

Parameter Count: 2

Parameter 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
1	1	`[[#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; '''
1	2	`[[#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; '''
2	1	`[[#601862c0]]`	"Reading an empty file"
2	2	`[[#601862c0]]`	"Repeated names with a TAXA block"