refactored project and added task_info/ dir

bsc-life · Nov 19, 2024 · a5ce49c · a5ce49c
1 parent 228db1c
commit a5ce49c
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Showing 22 changed files with 34 additions and 33 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,8 +1,7 @@
-mteapy/notebooks/
+notebooks/
 
 .pytest_cache
-mteapy/__pycache__
-mteapy/cmds/__pycache__
-mteapy/tests/__pycache__
-mteapy/mteapy.egg-info/
-mteapy.egg-info/
+tests/__pycache__
+src/mteapy/__pycache__
+src/mteapy/cmds/__pycache__
+src/mteapy.egg-info/
diff --git a/mteapy/data/HumanGEM.xml.gz → src/data/HumanGEM.xml.gz b/mteapy/data/HumanGEM.xml.gz → src/data/HumanGEM.xml.gz
diff --git a/.../data/HumanGEM_essential_genes_matrix.tsv → src/data/HumanGEM_essential_genes_matrix.tsv b/.../data/HumanGEM_essential_genes_matrix.tsv → src/data/HumanGEM_essential_genes_matrix.tsv
diff --git a/mteapy/data/HumanGEM_genes.tsv → src/data/HumanGEM_genes.tsv b/mteapy/data/HumanGEM_genes.tsv → src/data/HumanGEM_genes.tsv
diff --git a/mteapy/data/HumanGEM_secretory.xml.gz → src/data/HumanGEM_secretory.xml.gz b/mteapy/data/HumanGEM_secretory.xml.gz → src/data/HumanGEM_secretory.xml.gz
diff --git a/src/data/task_metadata.tsv b/src/data/task_metadata.tsv
@@ -0,0 +1 @@
+../../task_info/task_metadata.tsv
diff --git a/src/data/task_metadata_sec.tsv b/src/data/task_metadata_sec.tsv
@@ -0,0 +1 @@
+../../task_info/task_metadata_sec.tsv
diff --git a/mteapy/data/task_structure_matrix.tsv → src/data/task_structure_matrix.tsv b/mteapy/data/task_structure_matrix.tsv → src/data/task_structure_matrix.tsv
diff --git a/mteapy/data/task_structure_matrix_sec.tsv → src/data/task_structure_matrix_sec.tsv b/mteapy/data/task_structure_matrix_sec.tsv → src/data/task_structure_matrix_sec.tsv
diff --git a/mteapy/cellfie.py → src/mteapy/cellfie.py b/mteapy/cellfie.py → src/mteapy/cellfie.py
diff --git a/mteapy/cmds/run_mtea.py → src/mteapy/cmds/run_mtea.py b/mteapy/cmds/run_mtea.py → src/mteapy/cmds/run_mtea.py
@@ -16,7 +16,7 @@
 def main() -> None:
 
     curdir = os.path.dirname(os.path.realpath(__file__))
-    with open(os.path.join(curdir, "../../logo_ascii.txt"), "r") as f:
+    with open(os.path.join(curdir, "../logo_ascii.txt"), "r") as f:
         logo = f.read()
         print(logo)
 
@@ -30,17 +30,17 @@ def main() -> None:
         print(f"{bc.CYAN}Cite CellFie:{bc.ENDC}\thttps://doi.org/10.1016/j.crmeth.2021.100040\n")
         exit(1)
 
-    if args.task_metadata:
-        task_metadata = pd.read_csv(os.path.join(curdir, "../data/task_metadata.tsv"), sep="\t", index_col=0)
-        task_metadata.to_csv("./task_metadata.tsv", sep="\t")
-        print("Downloaded metabolic task metadata at ./task_metadata.tsv\n")
-        exit(1)
+    # if args.task_metadata:
+    #     task_metadata = pd.read_csv(os.path.join(curdir, "../../data/task_metadata.tsv"), sep="\t", index_col=0)
+    #     task_metadata.to_csv("./task_metadata.tsv", sep="\t")
+    #     print("Downloaded metabolic task metadata at ./task_metadata.tsv\n")
+    #     exit(1)
 
-    if args.task_metadata_sec:
-        task_metadata_sec = pd.read_csv(os.path.join(curdir, "../data/task_metadata_sec.tsv"), sep="\t", index_col=0)
-        task_metadata_sec.to_csv("./task_metadata_sec.tsv", sep="\t")
-        print("Downloaded secretory metabolic task metadata at ./task_metadata_sec.tsv\n")
-        exit(1)
+    # if args.task_metadata_sec:
+    #     task_metadata_sec = pd.read_csv(os.path.join(curdir, "../../data/task_metadata_sec.tsv"), sep="\t", index_col=0)
+    #     task_metadata_sec.to_csv("./task_metadata_sec.tsv", sep="\t")
+    #     print("Downloaded secretory metabolic task metadata at ./task_metadata_sec.tsv\n")
+    #     exit(1)
 
 
     ###########################################
@@ -70,8 +70,8 @@ def main() -> None:
 
         # Reading in data and gene essentiality
         expr_data_df = pd.read_csv(args.dea_file, delimiter=args.sep)
-        task_metadata = pd.read_csv(os.path.join(curdir, "../data/task_metadata.tsv"), sep="\t")
-        gene_essentiality = pd.read_csv(os.path.join(curdir, "../data/HumanGEM_essential_genes_matrix.tsv"),\
+        task_metadata = pd.read_csv(os.path.join(curdir, "../../data/task_metadata.tsv"), sep="\t")
+        gene_essentiality = pd.read_csv(os.path.join(curdir, "../../data/HumanGEM_essential_genes_matrix.tsv"),\
                                         delimiter="\t", index_col=0)
 
         # Column names check
@@ -142,20 +142,20 @@ def main() -> None:
         # Reading in data, model and task structure
         # TODO: allow user to input their own metabolic model and task structures
         expr_data_df = pd.read_csv(args.dea_file, delimiter=args.sep)
-        task_metadata = pd.read_csv(os.path.join(curdir, "../data/task_metadata.tsv"), sep="\t")
-        task_structure = pd.read_csv(os.path.join(curdir, "../data/task_structure_matrix.tsv"), \
+        task_metadata = pd.read_csv(os.path.join(curdir, "../../data/task_metadata.tsv"), sep="\t")
+        task_structure = pd.read_csv(os.path.join(curdir, "../../data/task_structure_matrix.tsv"), \
                                      sep="\t", index_col=0)
 
         print("Loading metabolic model", end=" ")
         if args.secretory_flag:
-            model = read_sbml_model(os.path.join(curdir, "../data/HumanGEM_secretory.xml.gz"))
-            task_metadata_sec = pd.read_csv(os.path.join(curdir, "../data/task_metadata_sec.tsv"), sep="\t")
+            model = read_sbml_model(os.path.join(curdir, "../../data/HumanGEM_secretory.xml.gz"))
+            task_metadata_sec = pd.read_csv(os.path.join(curdir, "../../data/task_metadata_sec.tsv"), sep="\t")
             task_metadata = pd.concat([task_metadata, task_metadata_sec])
-            task_structure_sec = pd.read_csv(os.path.join(curdir, "../data/task_structure_matrix_sec.tsv"), \
+            task_structure_sec = pd.read_csv(os.path.join(curdir, "../../data/task_structure_matrix_sec.tsv"), \
                                              sep="\t", index_col=0)
             task_structure = pd.concat([task_structure, task_structure_sec]).fillna(0)
         else:
-            model = read_sbml_model(os.path.join(curdir, "../data/HumanGEM.xml.gz"))
+            model = read_sbml_model(os.path.join(curdir, "../../data/HumanGEM.xml.gz"))
         print("- OK.")
 
         # Column names check
@@ -225,20 +225,20 @@ def main() -> None:
 
         # Reading in data
         expr_data_df = pd.read_csv(args.expr_file, delimiter=args.sep)
-        # task_metadata = pd.read_csv(os.path.join(curdir, "../data/task_metadata.tsv"), sep="\t")
-        task_structure = pd.read_csv(os.path.join(curdir, "../data/task_structure_matrix.tsv"), \
+        # task_metadata = pd.read_csv(os.path.join(curdir, "../../data/task_metadata.tsv"), sep="\t")
+        task_structure = pd.read_csv(os.path.join(curdir, "../../data/task_structure_matrix.tsv"), \
                                      sep="\t", index_col=0)
 
         print("Loading metabolic model", end=" ")
         if args.secretory_flag:
-            model = read_sbml_model(os.path.join(curdir, "../data/HumanGEM_secretory.xml.gz"))
-            # task_metadata_sec = pd.read_csv(os.path.join(curdir, "../data/task_metadata_sec.tsv"), sep="\t")
+            model = read_sbml_model(os.path.join(curdir, "../../data/HumanGEM_secretory.xml.gz"))
+            # task_metadata_sec = pd.read_csv(os.path.join(curdir, "../../data/task_metadata_sec.tsv"), sep="\t")
             # task_metadata = pd.concat([task_metadata, task_metadata_sec])
-            task_structure_sec = pd.read_csv(os.path.join(curdir, "../data/task_structure_matrix_sec.tsv"), \
+            task_structure_sec = pd.read_csv(os.path.join(curdir, "../../data/task_structure_matrix_sec.tsv"), \
                                              sep="\t", index_col=0)
             task_structure = pd.concat([task_structure, task_structure_sec]).fillna(0)
         else:
-            model = read_sbml_model(os.path.join(curdir, "../data/HumanGEM.xml.gz"))
+            model = read_sbml_model(os.path.join(curdir, "../../data/HumanGEM.xml.gz"))
         print("- OK.")
 
         # Column names check

diff --git a/mteapy/colors.py → src/mteapy/colors.py b/mteapy/colors.py → src/mteapy/colors.py
diff --git a/logo_ascii.txt → src/mteapy/logo_ascii.txt b/logo_ascii.txt → src/mteapy/logo_ascii.txt
diff --git a/mteapy/parser.py → src/mteapy/parser.py b/mteapy/parser.py → src/mteapy/parser.py
@@ -31,9 +31,9 @@ def mtea_parser():
 
     parser.add_argument("-c", "--cite", action="store_true", dest="citation_flag", help="prints information regarding citation of methods")
 
-    parser.add_argument("-t", "--task_metadata", action="store_true", dest="task_metadata", help="saves metabolic task metadata into current directory")
+    # parser.add_argument("-t", "--task_metadata", action="store_true", dest="task_metadata", help="saves metabolic task metadata into current directory")
 
-    parser.add_argument("-s", "--task_metadata_sec", action="store_true", dest="task_metadata_sec", help="saves secretory metabolic task metadata into current directory")
+    # parser.add_argument("-s", "--task_metadata_sec", action="store_true", dest="task_metadata_sec", help="saves secretory metabolic task metadata into current directory")
 
     subparser = parser.add_subparsers(title="commands", required=False, dest="command")
 

diff --git a/mteapy/tide.py → src/mteapy/tide.py b/mteapy/tide.py → src/mteapy/tide.py
diff --git a/mteapy/utils.py → src/mteapy/utils.py b/mteapy/utils.py → src/mteapy/utils.py
diff --git a/mteapy/data/task_metadata.tsv → task_info/task_metadata.tsv b/mteapy/data/task_metadata.tsv → task_info/task_metadata.tsv
diff --git a/mteapy/data/task_metadata_sec.tsv → task_info/task_metadata_sec.tsv b/mteapy/data/task_metadata_sec.tsv → task_info/task_metadata_sec.tsv
diff --git a/mteapy/tests/data/mask_lfc_test_expected.tsv → tests/data/mask_lfc_test_expected.tsv b/mteapy/tests/data/mask_lfc_test_expected.tsv → tests/data/mask_lfc_test_expected.tsv
diff --git a/mteapy/tests/data/mask_lfc_test_input.tsv → tests/data/mask_lfc_test_input.tsv b/mteapy/tests/data/mask_lfc_test_input.tsv → tests/data/mask_lfc_test_input.tsv
diff --git a/mteapy/tests/test_tide.py → tests/test_tide.py b/mteapy/tests/test_tide.py → tests/test_tide.py
diff --git a/mteapy/tests/test_utils.py → tests/test_utils.py b/mteapy/tests/test_utils.py → tests/test_utils.py