napistu 0.3.2.dev1__tar.gz → 0.3.4__tar.gz

{napistu-0.3.2.dev1 → napistu-0.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napistu
-Version: 0.3.2.dev1
+Version: 0.3.4
 Summary: Connecting high-dimensional data to curated pathways
 Home-page: https://github.com/napistu/napistu-py
 Author: Sean Hackett
@@ -19,7 +19,7 @@ Requires-Dist: Jinja2
 Requires-Dist: PyYAML<7.0.0,>=6.0.0
 Requires-Dist: click<9.0.0,>=8.0.0
 Requires-Dist: click-logging
-Requires-Dist: fs<3.0.0,>=2.4.0
+Requires-Dist: fs<3.0.0,>=2.4.16
 Requires-Dist: fs-gcsfs<2.0.0,>=1.5.0
 Requires-Dist: igraph
 Requires-Dist: matplotlib<4.0.0,>=3.5.0

{napistu-0.3.2.dev1 → napistu-0.3.4}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = napistu
-version = 0.3.2.dev1
+version = 0.3.4
 description = Connecting high-dimensional data to curated pathways
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -25,7 +25,7 @@ install_requires =
 	PyYAML>=6.0.0,<7.0.0
 	click>=8.0.0,<9.0.0
 	click-logging
-	fs>=2.4.0,<3.0.0
+	fs>=2.4.16,<3.0.0
 	fs-gcsfs>=1.5.0,<2.0.0
 	igraph
 	matplotlib>=3.5.0,<4.0.0

{napistu-0.3.2.dev1 → napistu-0.3.4}/src/napistu/constants.py

@@ -403,12 +403,6 @@ ONTOLOGIES = SimpleNamespace(
 
 ONTOLOGIES_LIST = list(ONTOLOGIES.__dict__.values())
 
-CHARACTERISTIC_COMPLEX_ONTOLOGIES = [
-    ONTOLOGIES.ENSEMBL_GENE,
-    ONTOLOGIES.NCBI_ENTREZ_GENE,
-    ONTOLOGIES.MIRBASE,
-]
-
 ONTOLOGY_SPECIES_ALIASES = {
     ONTOLOGIES.NCBI_ENTREZ_GENE: {"ncbigene", "ncbi_gene"},
     ONTOLOGIES.ENSEMBL_GENE: {"ensembl_gene_id"},
@@ -436,83 +430,3 @@ ENSEMBL_PREFIX_TO_ONTOLOGY = {
     "ENST": ONTOLOGIES.ENSEMBL_TRANSCRIPT,
     "ENSP": ONTOLOGIES.ENSEMBL_PROTEIN,
 }
-
-COMPARTMENTS = {
-    "NUCLEOPLASM": "nucleoplasm",
-    "CYTOPLASM": "cytoplasm",
-    "CELLULAR_COMPONENT": "cellular_component",
-    "CYTOSOL": "cytosol",
-    "MITOCHONDRIA": "mitochondria",
-    "MITOMEMBRANE": "mitochondrial membrane",
-    "INNERMITOCHONDRIA": "inner mitochondria",
-    "MITOMATRIX": "mitochondrial matrix",
-    "ENDOPLASMICRETICULUM": "endoplasmic reticulum",
-    "ERMEMBRANE": "endoplasmic reticulum membrane",
-    "ERLUMEN": "endoplasmic reticulum lumen",
-    "GOLGIAPPARATUS": "golgi apparatus",
-    "GOLGIMEMBRANE": "golgi membrane",
-    "NUCLEUS": "nucleus",
-    "NUCLEARLUMEN": "nuclear lumen",
-    "NUCLEOLUS": "nucleolus",
-    "LYSOSOME": "lysosome",
-    "PEROXISOME": "peroxisome",
-    "EXTRACELLULAR": "extracellular",
-}
-
-COMPARTMENT_ALIASES = {
-    "NUCLEOPLASM": ["nucleoplasm", "Nucleoplasm"],
-    "CYTOPLASM": ["cytoplasm", "Cytoplasm"],
-    "CELLULAR_COMPONENT": ["cellular_component", "Cellular_component"],
-    "CYTOSOL": ["cytosol", "Cytosol"],
-    "MITOCHONDRIA": ["mitochondria", "Mitochondria"],
-    "MITOMEMBRANE": ["mitochondrial membrane", "Mitochondrial membrane"],
-    "INNERMITOCHONDRIA": [
-        "inner mitochondria",
-        "Inner mitochondria",
-        "inner mitochondrial compartment",
-    ],
-    "MITOMATRIX": [
-        "mitochondrial matrix",
-        "Mitochondrial matrix",
-        "mitochondrial lumen",
-        "Mitochondrial lumen",
-    ],
-    "ENDOPLASMICRETICULUM": ["endoplasmic reticulum", "Endoplasmic reticulum"],
-    "ERMEMBRANE": ["endoplasmic reticulum membrane", "Endoplasmic reticulum membrane"],
-    "ERLUMEN": ["endoplasmic reticulum lumen", "Endoplasmic reticulum lumen"],
-    "GOLGIAPPARATUS": ["golgi apparatus", "Golgi apparatus"],
-    "GOLGIMEMBRANE": ["Golgi membrane", "golgi membrane"],
-    "NUCLEUS": ["nucleus", "Nucleus"],
-    "NUCLEARLUMEN": ["nuclear lumen", "Nuclear lumen"],
-    "NUCLEOLUS": ["nucleolus", "Nucleolus"],
-    "LYSOSOME": ["lysosome", "Lysosome"],
-    "PEROXISOME": ["peroxisome", "Peroxisome", "peroxisome/glyoxysome"],
-    "EXTRACELLULAR": [
-        "extracellular",
-        "Extracellular",
-        "extracellular space",
-        "Extracellular space",
-    ],
-}
-
-COMPARTMENTS_GO_TERMS = {
-    "NUCLEOPLASM": "GO:0005654",
-    "CELLULAR_COMPONENT": "GO:0005575",
-    "CYTOPLASM": "GO:0005737",
-    "CYTOSOL": "GO:0005829",
-    "MITOCHONDRIA": "GO:0005739",
-    "MITOMEMBRANE": "GO:0031966",
-    "INNERMITOCHONDRIA": "GO:0005743",
-    "MITOMATRIX": "GO:0005759",
-    "ENDOPLASMICRETICULUM": "GO:0005783",
-    "ERMEMBRANE": "GO:0005789",
-    "ERLUMEN": "GO:0005788",
-    "GOLGIAPPARATUS": "GO:0005794",
-    "GOLGIMEMBRANE": "GO:0000139",
-    "NUCLEUS": "GO:0005634",
-    "NUCLEARLUMEN": "GO:0031981",
-    "NUCLEOLUS": "GO:0005730",
-    "LYSOSOME": "GO:0005764",
-    "PEROXISOME": "GO:0005777",
-    "EXTRACELLULAR": "GO:0005615",
-}

{napistu-0.3.2.dev1 → napistu-0.3.4}/src/napistu/ingestion/constants.py

@@ -19,7 +19,6 @@ PROTEINATLAS_DEFS = SimpleNamespace(
     GENE="Gene",
 )
 
-
 # GTEx
 GTEX_RNASEQ_EXPRESSION_URL = "https://storage.googleapis.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct.gz"
 
@@ -92,42 +91,19 @@ REACTOME_PATHWAY_INDEX_COLUMNS = ["file", "source", "species", "pathway_id", "na
 REACTOME_PATHWAY_LIST_COLUMNS = ["pathway_id", "name", "species"]
 
 # SBML
-SMBL_ERROR_NUMBER = "error_number"
-SMBL_ERROR_CATEGORY = "category"
-SMBL_ERROR_SEVERITY = "severity"
-SMBL_ERROR_DESCRIPTION = "description"
-SMBL_ERROR_MESSAGE = "message"
-
-SMBL_SUMMARY_PATHWAY_NAME = "Pathway Name"
-SMBL_SUMMARY_PATHWAY_ID = "Pathway ID"
-SMBL_SUMMARY_N_SPECIES = "# of Species"
-SMBL_SUMMARY_N_REACTIONS = "# of Reactions"
-SMBL_SUMMARY_COMPARTMENTS = "Compartments"
-
-SMBL_REACTION_DICT_ID = "r_id"
-SMBL_REACTION_DICT_NAME = "r_name"
-SMBL_REACTION_DICT_IDENTIFIERS = "r_Identifiers"
-SMBL_REACTION_DICT_SOURCE = "r_Source"
-SMBL_REACTION_DICT_IS_REVERSIBLE = "r_isreversible"
-
-SMBL_REACTION_SPEC_RSC_ID = "rsc_id"
-SMBL_REACTION_SPEC_SC_ID = "sc_id"
-SMBL_REACTION_SPEC_STOICHIOMETRY = "stoichiometry"
-SMBL_REACTION_SPEC_SBO_TERM = "sbo_term"
-
-SBML_COMPARTMENT_DICT_ID = "c_id"
-SBML_COMPARTMENT_DICT_NAME = "c_name"
-SBML_COMPARTMENT_DICT_IDENTIFIERS = "c_Identifiers"
-SBML_COMPARTMENT_DICT_SOURCE = "c_Source"
-
-SBML_SPECIES_DICT_ID = "s_id"
-SBML_SPECIES_DICT_NAME = "s_name"
-SBML_SPECIES_DICT_IDENTIFIERS = "s_Identifiers"
-
-SBML_COMPARTMENTALIZED_SPECIES_DICT_NAME = "sc_name"
-SBML_COMPARTMENTALIZED_SPECIES_DICT_SOURCE = "sc_Source"
-
-SBML_REACTION_ATTR_GET_GENE_PRODUCT = "getGeneProduct"
+SBML_DEFS = SimpleNamespace(
+    ERROR_NUMBER="error_number",
+    ERROR_CATEGORY="category",
+    ERROR_SEVERITY="severity",
+    ERROR_DESCRIPTION="description",
+    ERROR_MESSAGE="message",
+    SUMMARY_PATHWAY_NAME="Pathway Name",
+    SUMMARY_PATHWAY_ID="Pathway ID",
+    SUMMARY_N_SPECIES="# of Species",
+    SUMMARY_N_REACTIONS="# of Reactions",
+    SUMMARY_COMPARTMENTS="Compartments",
+    REACTION_ATTR_GET_GENE_PRODUCT="getGeneProduct",
+)
 
 # STRING
 STRING_URL_EXPRESSIONS = {
@@ -178,3 +154,96 @@ YEAST_IDEA_PUBMED_ID = "32181581"  # ids are characters by convention
 # Identifiers ETL
 
 IDENTIFIERS_ETL_YEAST_HEADER_REGEX = "__________"
+
+COMPARTMENTS = SimpleNamespace(
+    NUCLEOPLASM="nucleoplasm",
+    CYTOPLASM="cytoplasm",
+    CELLULAR_COMPONENT="cellular_component",
+    CYTOSOL="cytosol",
+    MITOCHONDRIA="mitochondria",
+    MITOMEMBRANE="mitochondrial membrane",
+    INNERMITOCHONDRIA="inner mitochondria",
+    MITOMATRIX="mitochondrial matrix",
+    ENDOPLASMICRETICULUM="endoplasmic reticulum",
+    ERMEMBRANE="endoplasmic reticulum membrane",
+    ERLUMEN="endoplasmic reticulum lumen",
+    GOLGIAPPARATUS="golgi apparatus",
+    GOLGIMEMBRANE="golgi membrane",
+    NUCLEUS="nucleus",
+    NUCLEARLUMEN="nuclear lumen",
+    NUCLEOLUS="nucleolus",
+    LYSOSOME="lysosome",
+    PEROXISOME="peroxisome",
+    EXTRACELLULAR="extracellular",
+)
+
+GENERIC_COMPARTMENT = COMPARTMENTS.CELLULAR_COMPONENT
+EXCHANGE_COMPARTMENT = COMPARTMENTS.CYTOSOL
+VALID_COMPARTMENTS = list(COMPARTMENTS.__dict__.values())
+
+COMPARTMENT_ALIASES = {
+    COMPARTMENTS.NUCLEOPLASM: ["nucleoplasm", "Nucleoplasm"],
+    COMPARTMENTS.CYTOPLASM: ["cytoplasm", "Cytoplasm"],
+    COMPARTMENTS.CELLULAR_COMPONENT: ["cellular_component", "Cellular_component"],
+    COMPARTMENTS.CYTOSOL: ["cytosol", "Cytosol"],
+    COMPARTMENTS.MITOCHONDRIA: ["mitochondria", "Mitochondria"],
+    COMPARTMENTS.MITOMEMBRANE: ["mitochondrial membrane", "Mitochondrial membrane"],
+    COMPARTMENTS.INNERMITOCHONDRIA: [
+        "inner mitochondria",
+        "Inner mitochondria",
+        "inner mitochondrial compartment",
+    ],
+    COMPARTMENTS.MITOMATRIX: [
+        "mitochondrial matrix",
+        "Mitochondrial matrix",
+        "mitochondrial lumen",
+        "Mitochondrial lumen",
+    ],
+    COMPARTMENTS.ENDOPLASMICRETICULUM: [
+        "endoplasmic reticulum",
+        "Endoplasmic reticulum",
+    ],
+    COMPARTMENTS.ERMEMBRANE: [
+        "endoplasmic reticulum membrane",
+        "Endoplasmic reticulum membrane",
+    ],
+    COMPARTMENTS.ERLUMEN: [
+        "endoplasmic reticulum lumen",
+        "Endoplasmic reticulum lumen",
+    ],
+    COMPARTMENTS.GOLGIAPPARATUS: ["golgi apparatus", "Golgi apparatus"],
+    COMPARTMENTS.GOLGIMEMBRANE: ["Golgi membrane", "golgi membrane"],
+    COMPARTMENTS.NUCLEUS: ["nucleus", "Nucleus"],
+    COMPARTMENTS.NUCLEARLUMEN: ["nuclear lumen", "Nuclear lumen"],
+    COMPARTMENTS.NUCLEOLUS: ["nucleolus", "Nucleolus"],
+    COMPARTMENTS.LYSOSOME: ["lysosome", "Lysosome"],
+    COMPARTMENTS.PEROXISOME: ["peroxisome", "Peroxisome", "peroxisome/glyoxysome"],
+    COMPARTMENTS.EXTRACELLULAR: [
+        "extracellular",
+        "Extracellular",
+        "extracellular space",
+        "Extracellular space",
+    ],
+}
+
+COMPARTMENTS_GO_TERMS = {
+    COMPARTMENTS.NUCLEOPLASM: "GO:0005654",
+    COMPARTMENTS.CELLULAR_COMPONENT: "GO:0005575",
+    COMPARTMENTS.CYTOPLASM: "GO:0005737",
+    COMPARTMENTS.CYTOSOL: "GO:0005829",
+    COMPARTMENTS.MITOCHONDRIA: "GO:0005739",
+    COMPARTMENTS.MITOMEMBRANE: "GO:0031966",
+    COMPARTMENTS.INNERMITOCHONDRIA: "GO:0005743",
+    COMPARTMENTS.MITOMATRIX: "GO:0005759",
+    COMPARTMENTS.ENDOPLASMICRETICULUM: "GO:0005783",
+    COMPARTMENTS.ERMEMBRANE: "GO:0005789",
+    COMPARTMENTS.ERLUMEN: "GO:0005788",
+    COMPARTMENTS.GOLGIAPPARATUS: "GO:0005794",
+    COMPARTMENTS.GOLGIMEMBRANE: "GO:0000139",
+    COMPARTMENTS.NUCLEUS: "GO:0005634",
+    COMPARTMENTS.NUCLEARLUMEN: "GO:0031981",
+    COMPARTMENTS.NUCLEOLUS: "GO:0005730",
+    COMPARTMENTS.LYSOSOME: "GO:0005764",
+    COMPARTMENTS.PEROXISOME: "GO:0005777",
+    COMPARTMENTS.EXTRACELLULAR: "GO:0005615",
+}