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amirhossein-haerian · Aug 18, 2024 · 6247016 · 6247016
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Showing 34 changed files with 12 additions and 4 deletions.
diff --git a/Data/.DS_Store → genepioneer/Data/.DS_Store b/Data/.DS_Store → genepioneer/Data/.DS_Store
diff --git a/Data/benchmark-data/CGC.txt → genepioneer/Data/benchmark-data/CGC.txt b/Data/benchmark-data/CGC.txt → genepioneer/Data/benchmark-data/CGC.txt
diff --git a/Data/benchmark-data/CTAT.txt → genepioneer/Data/benchmark-data/CTAT.txt b/Data/benchmark-data/CTAT.txt → genepioneer/Data/benchmark-data/CTAT.txt
diff --git a/Data/benchmark-data/HCD.txt → genepioneer/Data/benchmark-data/HCD.txt b/Data/benchmark-data/HCD.txt → genepioneer/Data/benchmark-data/HCD.txt
diff --git a/Data/benchmark-data/RULE.txt → genepioneer/Data/benchmark-data/RULE.txt b/Data/benchmark-data/RULE.txt → genepioneer/Data/benchmark-data/RULE.txt
diff --git a/...er-gene-data/Adrenal_network_features.csv → ...er-gene-data/Adrenal_network_features.csv b/...er-gene-data/Adrenal_network_features.csv → ...er-gene-data/Adrenal_network_features.csv
diff --git a/...er-gene-data/Bladder_network_features.csv → ...er-gene-data/Bladder_network_features.csv b/...er-gene-data/Bladder_network_features.csv → ...er-gene-data/Bladder_network_features.csv
diff --git a/...ncer-gene-data/Brain_network_features.csv → ...ncer-gene-data/Brain_network_features.csv b/...ncer-gene-data/Brain_network_features.csv → ...ncer-gene-data/Brain_network_features.csv
diff --git a/...cer-gene-data/Cervix_network_features.csv → ...cer-gene-data/Cervix_network_features.csv b/...cer-gene-data/Cervix_network_features.csv → ...cer-gene-data/Cervix_network_features.csv
diff --git a/...ncer-gene-data/Colon_network_features.csv → ...ncer-gene-data/Colon_network_features.csv b/...ncer-gene-data/Colon_network_features.csv → ...ncer-gene-data/Colon_network_features.csv
diff --git a/...ne-data/Corpus uteri_network_features.csv → ...ne-data/Corpus uteri_network_features.csv b/...ne-data/Corpus uteri_network_features.csv → ...ne-data/Corpus uteri_network_features.csv
diff --git a/...cer-gene-data/Kidney_network_features.csv → ...cer-gene-data/Kidney_network_features.csv b/...cer-gene-data/Kidney_network_features.csv → ...cer-gene-data/Kidney_network_features.csv
diff --git a/...ncer-gene-data/Liver_network_features.csv → ...ncer-gene-data/Liver_network_features.csv b/...ncer-gene-data/Liver_network_features.csv → ...ncer-gene-data/Liver_network_features.csv
diff --git a/...ncer-gene-data/Ovary_network_features.csv → ...ncer-gene-data/Ovary_network_features.csv b/...ncer-gene-data/Ovary_network_features.csv → ...ncer-gene-data/Ovary_network_features.csv
diff --git a/...r-gene-data/Prostate_network_features.csv → ...r-gene-data/Prostate_network_features.csv b/...r-gene-data/Prostate_network_features.csv → ...r-gene-data/Prostate_network_features.csv
diff --git a/...ancer-gene-data/Skin_network_features.csv → ...ancer-gene-data/Skin_network_features.csv b/...ancer-gene-data/Skin_network_features.csv → ...ancer-gene-data/Skin_network_features.csv
diff --git a/...er-gene-data/Thyroid_network_features.csv → ...er-gene-data/Thyroid_network_features.csv b/...er-gene-data/Thyroid_network_features.csv → ...er-gene-data/Thyroid_network_features.csv
diff --git a/Data/evaluated_modules_result.json → ...ioneer/Data/evaluated_modules_result.json b/Data/evaluated_modules_result.json → ...ioneer/Data/evaluated_modules_result.json
diff --git a/Data/module-data/Adrenal.json → genepioneer/Data/module-data/Adrenal.json b/Data/module-data/Adrenal.json → genepioneer/Data/module-data/Adrenal.json
diff --git a/Data/module-data/Bladder.json → genepioneer/Data/module-data/Bladder.json b/Data/module-data/Bladder.json → genepioneer/Data/module-data/Bladder.json
diff --git a/Data/module-data/Brain.json → genepioneer/Data/module-data/Brain.json b/Data/module-data/Brain.json → genepioneer/Data/module-data/Brain.json
diff --git a/Data/module-data/Cervix.json → genepioneer/Data/module-data/Cervix.json b/Data/module-data/Cervix.json → genepioneer/Data/module-data/Cervix.json
diff --git a/Data/module-data/Colon.json → genepioneer/Data/module-data/Colon.json b/Data/module-data/Colon.json → genepioneer/Data/module-data/Colon.json
diff --git a/Data/module-data/Corpus uteri.json → ...ioneer/Data/module-data/Corpus uteri.json b/Data/module-data/Corpus uteri.json → ...ioneer/Data/module-data/Corpus uteri.json
diff --git a/Data/module-data/Kidney.json → genepioneer/Data/module-data/Kidney.json b/Data/module-data/Kidney.json → genepioneer/Data/module-data/Kidney.json
diff --git a/Data/module-data/Liver.json → genepioneer/Data/module-data/Liver.json b/Data/module-data/Liver.json → genepioneer/Data/module-data/Liver.json
diff --git a/Data/module-data/Ovary.json → genepioneer/Data/module-data/Ovary.json b/Data/module-data/Ovary.json → genepioneer/Data/module-data/Ovary.json
diff --git a/Data/module-data/Prostate.json → genepioneer/Data/module-data/Prostate.json b/Data/module-data/Prostate.json → genepioneer/Data/module-data/Prostate.json
diff --git a/Data/module-data/Skin.json → genepioneer/Data/module-data/Skin.json b/Data/module-data/Skin.json → genepioneer/Data/module-data/Skin.json
diff --git a/Data/module-data/Thyroid.json → genepioneer/Data/module-data/Thyroid.json b/Data/module-data/Thyroid.json → genepioneer/Data/module-data/Thyroid.json
diff --git a/Data/output.json → genepioneer/Data/output.json b/Data/output.json → genepioneer/Data/output.json
diff --git a/genepioneer/gene_analysis.py b/genepioneer/gene_analysis.py
@@ -2,6 +2,7 @@
 import pandas as pd
 
 import networkx as nx
+import pkg_resources
 
 class GeneAnalysis:
 
@@ -15,14 +16,16 @@ def __init__(self, cancer_type, input_path):
 
 
     def load_genes(self):
-        df = pd.read_csv(f"../Data/cancer-gene-data/{self.cancer_type}_network_features.csv")
+        data_path = pkg_resources.resource_filename(__name__, f"Data/cancer-gene-data/{self.cancer_type}_network_features.csv")
+        df = pd.read_csv(data_path)
 
         gene_data = df.to_dict(orient='records')
 
         return gene_data
 
     def load_modules(self):
-        with open(f"../Data/module-data/{self.cancer_type}.json", 'r') as file:
+        data_path = pkg_resources.resource_filename(__name__, f"Data/module-data/{self.cancer_type}.json")
+        with open(data_path, 'r') as file:
             data = json.load(file)
 
         modules = {}

diff --git a/setup.py b/setup.py
@@ -21,12 +21,17 @@
         'scikit-learn',
         'igraph',
         'leidenalg',
-        'gprofiler'
+        'gprofiler',
+        'matplotlib',
+        'gprofiler-official'
     ],
     classifiers=[
         'Development Status :: 3 - Alpha',
         'Intended Audience :: Science/Research',
         'Topic :: Scientific/Engineering :: Bio-Informatics',
     ],
+    package_data={
+        'genepioneer': ['Data/**/*', 'Data/**/**/*'],  
+    },
     keywords='cancer, genomics, gene-analysis',
 )
diff --git a/tests/test_gene_analysis.py b/tests/test_gene_analysis.py
@@ -8,5 +8,5 @@
 # "Adrenal", "Bladder", "Brain", "Cervix", "Colon", "Corpus uteri", "Kidney", "Liver", "Ovary", "Prostate", "Skin", "Thyroid"
 cancers = ["Bladder"]
 
-gene_analysis = GeneAnalysis("Ovary", "../Data/benchmark-data/CGC.txt")
+gene_analysis = GeneAnalysis("Ovary", "../genepioneer/Data/benchmark-data/CGC.txt")
 gene_analysis.analyze_genes()