Commit 74fa282a authored by Jan Hoeckesfeld's avatar Jan Hoeckesfeld
Browse files

try 2 incorp master

parent 16d936e2
......@@ -72,6 +72,7 @@ rule calcLikelihoods:
likelihoods = 'data/auxiliary/{dataset}/{iterset}/kmers/{kmer}/{id}/likelihoods_cov.json',
unexpectedLikelihoods = 'data/auxiliary/{dataset}/{iterset}/kmers/{kmer}/{id}/unexpected_likelihoods_cov.json'
#diffs = 'data/auxiliary/kmers/{kmer}/{id}/kmer_diff.tsv'
priority: 0
log:
'logs/{dataset}/{iterset}/probabilistic/kmers/{kmer}/{id}/likelihoods_cov.log'
benchmark:
......@@ -91,6 +92,33 @@ rule calcLikelihoods:
shell:
'c_kmertools --e {input.expected} --c {params.cpus} --m 0 --o {input.observed} --kmererror {params.e} --d {params.deviationCutoff} --target {output.likelihoods} --unexpected {output.unexpectedLikelihoods} --log {log} --itersetType {params.itersetType} --hammingdist {input.V_kmers_distances} --kmersindex {input.V_kmers}'
rule calcLikelihoods_master:
input:
expected = 'data/auxiliary/{dataset}/kmers/{kmer}/{id}/expected_counts.json',
observed = 'data/auxiliary/{dataset}/kmers/{kmer}/{id}/alignment.counts.json',
kmerError = 'data/auxiliary/{dataset}/kmers/{kmer}/{id}/kmer_error.txt',
kmerCoverageEstimate = determineKmerCoverageEstimateFile()
output:
likelihoods = 'data/auxiliary/{dataset}/master/kmers/{kmer}/{id}/likelihoods_cov.json',
unexpectedLikelihoods = 'data/auxiliary/{dataset}/master/kmers/{kmer}/{id}/unexpected_likelihoods_cov.json'
#diffs = 'data/auxiliary/kmers/{kmer}/{id}/kmer_diff.tsv'
priority: 1
log:
'logs/{dataset}/master/probabilistic/kmers/{kmer}/{id}/likelihoods_cov.log'
benchmark:
'benchmarks/{dataset}/master/probabilistic/kmers/{kmer}/{id}/calcLikelihoodsCoverageBasedModel.txt'
params:
e = (lambda wildcards,input : extractTsvValue(input.kmerError,0)),
deviationCutoff = (lambda wildcards,input : round(config['deviationCutoff']*extractCoverageEstimateFile(input.kmerCoverageEstimate,config))),
#cluster exectuion
cpus = '1',
mem = '4G',
gpus = '0',
walltime = '01:30:00'
singularity:
'docker://phspo/ckmertools:latest'
shell:
'c_kmertools --e {input.expected} --c {params.cpus} --m 0 --o {input.observed} --kmererror {params.e} --d {params.deviationCutoff} --target {output.likelihoods} --unexpected {output.unexpectedLikelihoods} --log {log}'
rule calcLikelihoods_Generative:
input:
......
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