Mercurial > repos > rnateam > graphclust_postprocessing
changeset 2:b8e32e577597 draft
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 9bc3c9b613d106098a78e16534897c88a3738c07
| author | rnateam |
|---|---|
| date | Sat, 24 Dec 2016 18:08:36 -0500 |
| parents | ed8c7191b322 |
| children | 79b9117aef01 |
| files | evaluation.py glob_report.xml |
| diffstat | 2 files changed, 29 insertions(+), 0 deletions(-) [+] |
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--- a/evaluation.py Thu Dec 22 09:06:48 2016 -0500 +++ b/evaluation.py Sat Dec 24 18:08:36 2016 -0500 @@ -1,6 +1,7 @@ import glob from os import system import re +from sklearn import metrics def sh(script): system("bash -c '%s'" % script) @@ -46,3 +47,29 @@ toWrite += listOfClasses[i] + "\t" + listOfClusters[i] + '\n' with open("RESULTS/fullTab.tabular", "w") as full: full.write(toWrite) + + +listOfClasses = [] +listOfClusters = [] +pattern = re.compile("^RF.*$") + + +if len(listOfClasses) > 0 and pattern.match(str(listOfClasses[0])): + with open("RESULTS/fullTab.tabular", "r") as tabF: + for line in tabF.readlines(): + listOfClasses.append(line.split()[0]) + listOfClusters.append(line.split()[1]) + + completeness_score = metrics.completeness_score(listOfClasses, listOfClusters) + homogeneity_score = metrics.homogeneity_score(listOfClasses, listOfClusters) + adjusted_rand_score = metrics.adjusted_rand_score(listOfClasses, listOfClusters) + adjusted_mutual_info_score = metrics.adjusted_mutual_info_score(listOfClasses, listOfClusters) + v_measure_score = metrics.v_measure_score(listOfClasses, listOfClusters) + + toWrite = "completeness_score : " + str(completeness_score) + "\n" + "homogeneity_score : " + str(homogeneity_score) + "\n" + "adjusted_rand_score : " +str(adjusted_rand_score) + "\n" + "adjusted_mutual_info_score : " + str(adjusted_mutual_info_score)+ "\n" + "v_measure_score : " + str(v_measure_score) + +else: + toWrite = "completeness_score : NA \nhomogeneity_score : NA \nadjusted_rand_score : NA \nadjusted_mutual_info_score : NA \nv_measure_score : NA" + +with open("RESULTS/evaluation.txt", "w") as fOut: + fOut.write(toWrite)
--- a/glob_report.xml Thu Dec 22 09:06:48 2016 -0500 +++ b/glob_report.xml Sat Dec 24 18:08:36 2016 -0500 @@ -2,6 +2,7 @@ <requirements> <requirement type="package" version="0.1">graphclust-wrappers</requirement> <requirement type="package" version='0.5'>perl-array-utils</requirement> + <requirement type="package" version='0.18.1'>scikit-learn</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -64,6 +65,7 @@ <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" /> <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" /> <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" /> + <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" /> <collection name="clusters" type="list" label="CLUSTERS"> <discover_datasets pattern="(?P<name>^.*\.all$)" directory="RESULTS" /> </collection>