Commit 0517afb9 authored by Jan Hoeckesfeld's avatar Jan Hoeckesfeld
Browse files

parameter to change the likelihood-iterset added

parent c7246bda
.vs/
out/
.idea/
\ No newline at end of file
......@@ -95,3 +95,7 @@ blast_word_size : 4
blast_word_size_hypProtA : 11
blast_e_value : 1.0e-40
blast_e_value_hypProtA : 1.0e-50
### Choose Iterationset to determine likelihoods
iterationset : observation
......@@ -7,6 +7,15 @@ def determineKmerCoverageEstimateFile():
elif config['kmerCoverageEstimationMethod'] == 'countPoisson':
return 'data/auxiliary/'+config['input_folder']+'/kmers/{kmer}/{id}/coverage_estimate_kmercountbased.txt'
# TODO: will need arg spatyp later
def determineIterationset():
if config['iterationset'] == 'observation':
return 'data/auxiliary/'+config['input_folder']+'/kmers/{kmer}/{id}/alignment.counts.json'
elif config['iterationset'] == 'spatype':
return '?'
elif config['iterationset'] == 'database':
return '?'
# Returns the corresponding ground truth spa-type for a given file (sample) id
def getGroundTruthType(fid):
with open('data/input/groundTruth.tsv','r') as gtfile:
......
......@@ -64,6 +64,7 @@ rule calcLikelihoods:
input:
expected = 'data/auxiliary/'+config['input_folder']+'/kmers/{kmer}/{id}/expected_counts.json',
observed = 'data/auxiliary/'+config['input_folder']+'/kmers/{kmer}/{id}/alignment.counts.json',
iterationset = determineIterationset({id}}),
kmerError = 'data/auxiliary/'+config['input_folder']+'/kmers/{kmer}/{id}/kmer_error.txt',
kmerCoverageEstimate = determineKmerCoverageEstimateFile()
output:
......
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