Commit fb0a29fd authored by Jan Hoeckesfeld's avatar Jan Hoeckesfeld
Browse files

added master

parent 1686cc40
......@@ -86,10 +86,10 @@ rule calcLikelihoods:
gpus = '0',
walltime = lambda wildcards, attempt: '01:00:00'
singularity:
'singularity_container/ckmertools_iterset.sif'
lambda wildcards: 'docker://phspo/ckmertools:latest' if wildcards.iterset=="master" else 'singularity_container/ckmertools_iterset.sif'
#'docker://phspo/ckmertools:iterationset-tests'
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}'
lambda wildcards: '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}' if wildcards.iterset=="master" else '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_Generative:
......
......@@ -61,10 +61,10 @@ def summarize(input,benchmarks,groundTruthFile,output):
if line[0] in ids:
results["expected"][line[0]] = line[1]
cols_tuples = [("observed_" + i + "_" + k, "estimate_" + i + "_" + k, i + "_" + k + "_time", i + "_" + k + "_cpu%") for i in results.keys() for k in results[i].keys()]
cols_tuples = [("observed" + i + k, "estimate" + i + k, i + k + "time", i + k + "cpu%") for i in results.keys() for k in results[i].keys()]
table_col_names = ["expected"] + [c for ct in cols_tuples for c in ct]
with open(output,'w') as outfile:
outfile.write(",".join(table_col_names) + '\n')
outfile.write("; ".join(table_col_names) + '\n')
for i in ids:
col = [results["expected"][i]]
......@@ -76,6 +76,6 @@ def summarize(input,benchmarks,groundTruthFile,output):
col.append(get_in(results,[iterset,kmer,i,"prob"]))
col.append(get_in(results,[iterset,kmer,i,"time"]))
col.append(get_in(results,[iterset,kmer,i,"mean_load"]))
outfile.write(", ".join(col) + '\n')
outfile.write("; ".join(col) + '\n')
summarize(snakemake.input['results'],snakemake.input['benchmarks'],snakemake.input["groundTruthFile"],snakemake.output['summary'])
\ No newline at end of file
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