Mercurial > repos > bimib > marea
changeset 12:3d77287caf22 draft
Uploaded
| author | bimib |
|---|---|
| date | Wed, 13 Feb 2019 05:08:25 -0500 |
| parents | d185506631e1 |
| children | e96f3b85e5a0 |
| files | Marea/local/Recon_rules.p Marea/marea.py Marea/marea.xml Marea/marea_cluster.py Marea/marea_cluster.xml Marea/marea_macros.xml Marea_beckup_13022019.zip |
| diffstat | 6 files changed, 8 insertions(+), 15 deletions(-) [+] |
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--- a/Marea/marea.py Wed Feb 13 05:06:53 2019 -0500 +++ b/Marea/marea.py Wed Feb 13 05:08:25 2019 -0500 @@ -456,7 +456,7 @@ elif l[0] == 'or': flag = False break - if flag == True: #when there are only AND in list + if flag == True: #se ci sono solo AND nella lista tmp.extend(tmpAnd) elif flag == False: tmp.append(tmpAnd)
--- a/Marea/marea.xml Wed Feb 13 05:06:53 2019 -0500 +++ b/Marea/marea.xml Wed Feb 13 05:08:25 2019 -0500 @@ -83,8 +83,8 @@ </when> </conditional> <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> - <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold:" help="min value 0" /> - <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold:" help="min value 1" /> + <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold" help="min value 0" /> + <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold" help="min value 1" /> </inputs> <outputs>
--- a/Marea/marea_cluster.py Wed Feb 13 05:06:53 2019 -0500 +++ b/Marea/marea_cluster.py Wed Feb 13 05:08:25 2019 -0500 @@ -540,22 +540,13 @@ def f_cluster(resolve_rules): os.makedirs('cluster_out') args = process_args(sys.argv) - k_min = args.k_min - k_max = args.k_max - if k_min > k_max: - warning('k range boundaries inverted.\n') - tmp = k_min - k_min = k_max - k_max = tmp - else: - warning('k range correct.\n') cluster_data = pd.DataFrame.from_dict(resolve_rules, orient = 'index') for i in cluster_data.columns: tmp = cluster_data[i][0] if tmp == None: cluster_data = cluster_data.drop(columns=[i]) distorsion = [] - for i in range(k_min, k_max+1): + for i in range(args.k_min, args.k_max+1): tmp_kmeans = KMeans(n_clusters = i, n_init = 100, max_iter = 300, @@ -568,7 +559,7 @@ classe.to_csv(dest, sep = '\t', index = False, header = ['Patient_ID', 'Class']) plt.figure(0) - plt.plot(range(k_min, k_max+1), distorsion, marker = 'o') + plt.plot(range(args.k_min, args.k_max+1), distorsion, marker = 'o') plt.xlabel('Number of cluster') plt.ylabel('Distorsion') plt.savefig(args.elbow, dpi = 240, format = 'pdf') @@ -585,6 +576,8 @@ def main(): args = process_args(sys.argv) + if args.k_min > args.k_max: + sys.exit('Execution aborted: max cluster > min cluster') if args.rules_selector == 'HMRcore': recon = pk.load(open(args.tool_dir + '/local/HMRcore_rules.p', 'rb')) elif args.rules_selector == 'Recon':
--- a/Marea/marea_macros.xml Wed Feb 13 05:06:53 2019 -0500 +++ b/Marea/marea_macros.xml Wed Feb 13 05:08:25 2019 -0500 @@ -66,7 +66,7 @@ <token name="@REFERENCE@"> -This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_. +This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_. Development team: Irene Sala, Luca Rosato, Davide Maspero, Chiara Damiani. .. _BIMIB: http://sito di bio.org .. _Department of Informatics, Systems and Communications: http://www.disco.unimib.it/go/Home/English