CloneSet84


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Clone
Mass
Clones in
CloneSet
Parameter
Count
Clone
Similarity
Syntax Category
[Sequence Length]
4740.968or_test
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
1479
Bio/Align/Applications/_Prank.py
2496
Bio/Align/Applications/_Prank.py
34101
Bio/Align/Applications/_Prank.py
44162
Bio/Align/Applications/_Prank.py
54167
Bio/Align/Applications/_Prank.py
64173
Bio/Align/Applications/_Prank.py
74179
Bio/Align/Applications/_Prank.py
Clone Instance
1
Line Count
4
Source Line
79
Source File
Bio/Align/Applications/_Prank.py

            #-gaprate=# [gap opening rate; default: dna 0.025 / prot 0.0025]
            _Option(["-gaprate","gaprate"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Gap opening rate. Default: dna 0.025 prot 0.0025")


Clone Instance
2
Line Count
4
Source Line
96
Source File
Bio/Align/Applications/_Prank.py

            #-kappa=# [ts/tv rate ratio; default:2]
            _Option(["-kappa","kappa"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Transition/transversion ratio. Default: 2")


Clone Instance
3
Line Count
4
Source Line
101
Source File
Bio/Align/Applications/_Prank.py

            #-rho=# [pur/pyr rate ratio; default:1]
            _Option(["-rho","rho"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Purine/pyrimidine ratio. Default: 1")


Clone Instance
4
Line Count
4
Source Line
162
Source File
Bio/Align/Applications/_Prank.py

            #-pwgenomicdist=# [distance for pairwise alignment; default: 0.3]
            _Option(["-pwgenomicdist","pwgenomicdist"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Distance for pairwise alignment. Default: 0.3")


Clone Instance
5
Line Count
4
Source Line
167
Source File
Bio/Align/Applications/_Prank.py

            #-scalebranches=# [scale branch lengths; default: dna 1 / prot 2]
            _Option(["-scalebranches","scalebranches"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Scale branch lengths. Default: dna 1 / prot 2")


Clone Instance
6
Line Count
4
Source Line
173
Source File
Bio/Align/Applications/_Prank.py

            #-fixedbranches=# [use fixed branch lengths]
            #Assume looking for a float
            _Option(["-fixedbranches","fixedbranches"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Use fixed branch lengths of input value")


Clone Instance
7
Line Count
4
Source Line
179
Source File
Bio/Align/Applications/_Prank.py

            #-maxbranches=# [set maximum branch length]
            #Assume looking for a float
            _Option(["-maxbranches","maxbranches"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Use maximum branch lengths of input value")


Clone AbstractionParameter Count: 4Parameter Bindings

#-maxbranches=# [set maximum branch length]
#-fixedbranches=# [use fixed branch lengths]
#Assume looking for a float
#-scalebranches=# [scale branch lengths; default: dna 1 / prot 2]
#-pwgenomicdist=# [distance for pairwise alignment; default: 0.3]
#-rho=# [pur/pyr rate ratio; default:1]
#-kappa=# [ts/tv rate ratio; default:2]
#-gaprate=# [gap opening rate; default: dna 0.025 / prot 0.0025]
_Option([ [[#variable4fdb96c0]], [[#variable5f4b3d40]]],["input"], lambda x:isinstance(x,types. [[#variable4fdb95e0]]),0, [[#variable4fdb9640]])
 

CloneAbstraction
Parameter Bindings
Parameter
Index
Clone
Instance
Parameter
Name
Value
11[[#4fdb96c0]]
"-maxbranches" 
12[[#4fdb96c0]]
"-fixedbranches" 
13[[#4fdb96c0]]
"-scalebranches" 
14[[#4fdb96c0]]
"-pwgenomicdist" 
15[[#4fdb96c0]]
"-rho" 
16[[#4fdb96c0]]
"-kappa" 
17[[#4fdb96c0]]
"-gaprate" 
21[[#5f4b3d40]]
"maxbranches" 
22[[#5f4b3d40]]
"fixedbranches" 
23[[#5f4b3d40]]
"scalebranches" 
24[[#5f4b3d40]]
"pwgenomicdist" 
25[[#5f4b3d40]]
"rho" 
26[[#5f4b3d40]]
"kappa" 
27[[#5f4b3d40]]
"gaprate" 
31[[#4fdb95e0]]
FloatType 
32[[#4fdb95e0]]
FloatType 
33[[#4fdb95e0]]
IntType 
34[[#4fdb95e0]]
FloatType 
35[[#4fdb95e0]]
IntType 
36[[#4fdb95e0]]
IntType 
37[[#4fdb95e0]]
FloatType 
41[[#4fdb9640]]
"Use maximum branch lengths of input value" 
42[[#4fdb9640]]
"Use fixed branch lengths of input value" 
43[[#4fdb9640]]
"Scale branch lengths. Default: dna 1 / prot 2" 
44[[#4fdb9640]]
"Distance for pairwise alignment. Default: 0.3" 
45[[#4fdb9640]]
"Purine/pyrimidine ratio. Default: 1" 
46[[#4fdb9640]]
"Transition/transversion ratio. Default: 2" 
47[[#4fdb9640]]
"Gap opening rate. Default: dna 0.025 prot 0.0025"