CloneSet33


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Clone
Mass
Clones in
CloneSet
Parameter
Count
Clone
Similarity
Syntax Category
[Sequence Length]
31450.957or_test
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
1341
Bio/Align/Applications/_Muscle.py
2448
Bio/Align/Applications/_Muscle.py
3452
Bio/Align/Applications/_Muscle.py
44143
Bio/Align/Applications/_Muscle.py
54149
Bio/Align/Applications/_Muscle.py
6260
Bio/Blast/Applications.py
72195
Bio/Blast/Applications.py
82197
Bio/Blast/Applications.py
92199
Bio/Blast/Applications.py
102201
Bio/Blast/Applications.py
112203
Bio/Blast/Applications.py
122239
Bio/Blast/Applications.py
13322
Bio/Sequencing/Applications/_Novoalign.py
14325
Bio/Sequencing/Applications/_Novoalign.py
Clone Instance
1
Line Count
3
Source Line
41
Source File
Bio/Align/Applications/_Muscle.py

            _Option(["-out","out"],["output","file"],None,0,"Output filename",0)


Clone Instance
2
Line Count
4
Source Line
48
Source File
Bio/Align/Applications/_Muscle.py

            _Option(["-in1","in1"],["input","file"],None,0,"First input filename for profile alignment",0)


Clone Instance
3
Line Count
4
Source Line
52
Source File
Bio/Align/Applications/_Muscle.py

            _Option(["-in2","in2"],["input","file"],None,0,"Second input filename for a profile alignment",0)


Clone Instance
4
Line Count
4
Source Line
143
Source File
Bio/Align/Applications/_Muscle.py

            #log             File name            None.              Log file name (delete
            #                                                        existing file).
            _Option(["-log","log"],["output","file"],None,0,"Log file name",0)


Clone Instance
5
Line Count
4
Source Line
149
Source File
Bio/Align/Applications/_Muscle.py

            #loga            File name            None.              Log file name (append
            #                                                        to existing file).
            _Option(["-loga","loga"],["output","file"],None,0,"Log file name (append to existing file)",0)


Clone Instance
6
Line Count
2
Source Line
60
Source File
Bio/Blast/Applications.py

           _Option(["-O","seqalign_file"],["output","file"],None,0,"seqalign file to output.",False)


Clone Instance
7
Line Count
2
Source Line
195
Source File
Bio/Blast/Applications.py

           _Option(["-C","checkpoint_outfile"],["output","file"],None,0,"Output file for PSI-BLAST checkpointing.",False)


Clone Instance
8
Line Count
2
Source Line
197
Source File
Bio/Blast/Applications.py

           _Option(["-R","restart_infile"],["input","file"],None,0,"Input file for PSI-BLAST restart.",False)


Clone Instance
9
Line Count
2
Source Line
199
Source File
Bio/Blast/Applications.py

           _Option(["-k","hit_infile"],["input","file"],None,0,"Hit file for PHI-BLAST.",False)


Clone Instance
10
Line Count
2
Source Line
201
Source File
Bio/Blast/Applications.py

           _Option(["-Q","matrix_outfile"],["output","file"],None,0,"Output file for PSI-BLAST matrix in ASCII.",False)


Clone Instance
11
Line Count
2
Source Line
203
Source File
Bio/Blast/Applications.py

           _Option(["-B","align_infile"],["input","file"],None,0,"Input alignment file for PSI-BLAST restart.",False)


Clone Instance
12
Line Count
2
Source Line
239
Source File
Bio/Blast/Applications.py

           _Option(["-l","logfile"],["output","file"],None,0,"Logfile name.",False)


Clone Instance
13
Line Count
3
Source Line
22
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-d","database"],["input","file"],None,0,"database filename",0)


Clone Instance
14
Line Count
3
Source Line
25
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-f","readfile"],["input","file"],None,0,"read file",0)


Clone AbstractionParameter Count: 5Parameter Bindings

#log             File name            None.              Log file name (delete
#                                                        existing file).
#loga            File name            None.              Log file name (append
#                                                        to existing file).
_Option([ [[#variable71a585e0]], [[#variable71a58560]]],[ [[#variable71a58500]],"file"],None,0, [[#variable71a58480]], [[#variable71a583e0]])
 

CloneAbstraction
Parameter Bindings
Parameter
Index
Clone
Instance
Parameter
Name
Value
11[[#71a585e0]]
"-d" 
12[[#71a585e0]]
"-f" 
13[[#71a585e0]]
"-O" 
14[[#71a585e0]]
"-C" 
15[[#71a585e0]]
"-R" 
16[[#71a585e0]]
"-k" 
17[[#71a585e0]]
"-Q" 
18[[#71a585e0]]
"-B" 
19[[#71a585e0]]
"-l" 
110[[#71a585e0]]
"-out" 
111[[#71a585e0]]
"-in1" 
112[[#71a585e0]]
"-in2" 
113[[#71a585e0]]
"-log" 
114[[#71a585e0]]
"-loga" 
21[[#71a58560]]
"database" 
22[[#71a58560]]
"readfile" 
23[[#71a58560]]
"seqalign_file" 
24[[#71a58560]]
"checkpoint_outfile" 
25[[#71a58560]]
"restart_infile" 
26[[#71a58560]]
"hit_infile" 
27[[#71a58560]]
"matrix_outfile" 
28[[#71a58560]]
"align_infile" 
29[[#71a58560]]
"logfile" 
210[[#71a58560]]
"out" 
211[[#71a58560]]
"in1" 
212[[#71a58560]]
"in2" 
213[[#71a58560]]
"log" 
214[[#71a58560]]
"loga" 
31[[#71a58500]]
"input" 
32[[#71a58500]]
"input" 
33[[#71a58500]]
"output" 
34[[#71a58500]]
"output" 
35[[#71a58500]]
"input" 
36[[#71a58500]]
"input" 
37[[#71a58500]]
"output" 
38[[#71a58500]]
"input" 
39[[#71a58500]]
"output" 
310[[#71a58500]]
"output" 
311[[#71a58500]]
"input" 
312[[#71a58500]]
"input" 
313[[#71a58500]]
"output" 
314[[#71a58500]]
"output" 
41[[#71a58480]]
"database filename" 
42[[#71a58480]]
"read file" 
43[[#71a58480]]
"seqalign file to output." 
44[[#71a58480]]
"Output file for PSI-BLAST checkpointing." 
45[[#71a58480]]
"Input file for PSI-BLAST restart." 
46[[#71a58480]]
"Hit file for PHI-BLAST." 
47[[#71a58480]]
"Output file for PSI-BLAST matrix in ASCII." 
48[[#71a58480]]
"Input alignment file for PSI-BLAST restart." 
49[[#71a58480]]
"Logfile name." 
410[[#71a58480]]
"Output filename" 
411[[#71a58480]]
"First input filename for profile alignment" 
412[[#71a58480]]
"Second input filename for a profile alignment" 
413[[#71a58480]]
"Log file name" 
414[[#71a58480]]
"Log file name (append to existing file)" 
51[[#71a583e0]]
0 
52[[#71a583e0]]
0 
53[[#71a583e0]]
False 
54[[#71a583e0]]
False 
55[[#71a583e0]]
False 
56[[#71a583e0]]
False 
57[[#71a583e0]]
False 
58[[#71a583e0]]
False 
59[[#71a583e0]]
False 
510[[#71a583e0]]
0 
511[[#71a583e0]]
0 
512[[#71a583e0]]
0 
513[[#71a583e0]]
0 
514[[#71a583e0]]
0