Created gapfill.py #52

refinegems/gapfill.py

@@ -0,0 +1,24 @@
+# Function originally from refineGEMs.genecomp/refineGEMs.KEGG_analysis --- Modified
+def compare_gene_lists(gps_in_model: pd.DataFrame, db_genes: pd.DataFrame) -> pd.DataFrame:
+
+   in_db = db_genes.set_index('Locus_tag')
+   in_model = gps_in_model.set_index(0)
+   genes_in_db_not_in_model = in_db[~in_db.index.isin(in_model.index)]
+   return genes_in_db_not_in_model.reset_index()
+
+def get_genes_from_gff():
+   pass
+
+
+def compare_model_to_gff():
+   pass
+
+
+def get_related_metabs_reactions_blast():
+   pass
+
+
+def gapfill():
+   ''' Main function to gapfill a model with comparison to KEGG/BioCyc/(Genbank) GFF file
+   '''
+   pass