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| Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
|---|---|---|---|---|
| 17 | 4 | 5 | 0.969 | compound_stmt |
| Clone Abstraction | Parameter Bindings |
| Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
|---|---|---|---|
| 1 | 11 | 348 | Bio/PopGen/GenePop/Controller.py |
| 2 | 11 | 361 | Bio/PopGen/GenePop/Controller.py |
| 3 | 17 | 404 | Bio/PopGen/GenePop/Controller.py |
| 4 | 17 | 424 | Bio/PopGen/GenePop/Controller.py |
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def test_pop_hz_deficiency(self,fname,enum_test = True,dememorization = 10000,batches = 20,iterations = 5000):
"""Hardy-Weinberg test for heterozygote deficiency.
Returns a population iterator containg
A dictionary[locus]=(P-val, SE, Fis-WC, Fis-RH, steps)
Some loci have a None if the info is not available
SE might be none (for enumerations)
"""
return self._test_pop_hz_both(fname,1,".D",enum_test,dememorization,batches,iterations)
#1.2
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def test_pop_hz_excess(self,fname,enum_test = True,dememorization = 10000,batches = 20,iterations = 5000):
"""Hardy-Weinberg test for heterozygote deficiency.
Returns a population iterator containg
A dictionary[locus]=(P-val, SE, Fis-WC, Fis-RH, steps)
Some loci have a None if the info is not available
SE might be none (for enumerations)
"""
return self._test_pop_hz_both(fname,2,".E",enum_test,dememorization,batches,iterations)
#1.3 P file
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def test_global_hz_deficiency(self,fname,enum_test = True,dememorization = 10000,batches = 20,iterations = 5000):
"""Global Hardy-Weinberg test for heterozygote deficiency.
Returns a triple with:
An list per population containg
(pop_name, P-val, SE, switches)
Some pops have a None if the info is not available
SE might be none (for enumerations)
An list per loci containg
(locus_name, P-val, SE, switches)
Some loci have a None if the info is not available
SE might be none (for enumerations)
Overall results (P-val, SE, switches)
"""
return self._test_global_hz_both(fname,4,".DG",enum_test,dememorization,batches,iterations)
#1.5
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def test_global_hz_excess(self,fname,enum_test = True,dememorization = 10000,batches = 20,iterations = 5000):
"""Global Hardy-Weinberg test for heterozygote excess.
Returns a triple with:
An list per population containg
(pop_name, P-val, SE, switches)
Some pops have a None if the info is not available
SE might be none (for enumerations)
An list per loci containg
(locus_name, P-val, SE, switches)
Some loci have a None if the info is not available
SE might be none (for enumerations)
Overall results (P-val, SE, switches)
"""
return self._test_global_hz_both(fname,5,".EG",enum_test,dememorization,batches,iterations)
#2.1
|
| |||
def [[#variable71aafb80]](self,fname,enum_test = True,dememorization = 10000,batches = 20,iterations = 5000): [[#variable71aafb00]] return self. [[#variable71aafa80]](fname, [[#variable71aafa20]], [[#variable71aaf920]],enum_test,dememorization,batches,iterations) #2.1 #1.5 #1.3 P file #1.2 |
| CloneAbstraction |
| Parameter Index | Clone Instance | Parameter Name | Value |
|---|---|---|---|
| 1 | 1 | [[#71aafb80]] | test_global_hz_excess |
| 1 | 2 | [[#71aafb80]] | test_global_hz_deficiency |
| 1 | 3 | [[#71aafb80]] | test_pop_hz_excess |
| 1 | 4 | [[#71aafb80]] | test_pop_hz_deficiency |
| 2 | 1 | [[#71aafb00]] | """Global Hardy-Weinberg test for heterozygote excess.
Returns a triple with:
An list per population containg
(pop_name, P-val, SE, switches)
Some pops have a None if the info is not available
SE might be none (for enumerations)
An list per loci containg
(locus_name, P-val, SE, switches)
Some loci have a None if the info is not available
SE might be none (for enumerations)
Overall results (P-val, SE, switches)
""" |
| 2 | 2 | [[#71aafb00]] | """Global Hardy-Weinberg test for heterozygote deficiency.
Returns a triple with:
An list per population containg
(pop_name, P-val, SE, switches)
Some pops have a None if the info is not available
SE might be none (for enumerations)
An list per loci containg
(locus_name, P-val, SE, switches)
Some loci have a None if the info is not available
SE might be none (for enumerations)
Overall results (P-val, SE, switches)
""" |
| 2 | 3 | [[#71aafb00]] | """Hardy-Weinberg test for heterozygote deficiency.
Returns a population iterator containg
A dictionary[locus]=(P-val, SE, Fis-WC, Fis-RH, steps)
Some loci have a None if the info is not available
SE might be none (for enumerations)
""" |
| 2 | 4 | [[#71aafb00]] | """Hardy-Weinberg test for heterozygote deficiency.
Returns a population iterator containg
A dictionary[locus]=(P-val, SE, Fis-WC, Fis-RH, steps)
Some loci have a None if the info is not available
SE might be none (for enumerations)
""" |
| 3 | 1 | [[#71aafa80]] | _test_global_hz_both |
| 3 | 2 | [[#71aafa80]] | _test_global_hz_both |
| 3 | 3 | [[#71aafa80]] | _test_pop_hz_both |
| 3 | 4 | [[#71aafa80]] | _test_pop_hz_both |
| 4 | 1 | [[#71aafa20]] | 5 |
| 4 | 2 | [[#71aafa20]] | 4 |
| 4 | 3 | [[#71aafa20]] | 2 |
| 4 | 4 | [[#71aafa20]] | 1 |
| 5 | 1 | [[#71aaf920]] | ".EG" |
| 5 | 2 | [[#71aaf920]] | ".DG" |
| 5 | 3 | [[#71aaf920]] | ".E" |
| 5 | 4 | [[#71aaf920]] | ".D" |