updated cosmic and opentargets docs

Author: josephrich98

docs/src/en/opentargets.md

@@ -34,41 +34,8 @@ Note: Not compatible with the `tractability` and `depmap` resources.
 Path to the JSON file the results will be saved in, e.g. path/to/directory/results.json. Default: Standard out.  
 Python: `save=True` will save the output in the current working directory.
 
-**Optional filter arguments**
-
-`-fd` `--filter_disease` `disease_id`  
-Filter by disease ID, e.g. 'EFO_0000274'. *Only valid for the `drugs` resource.*
-
-`-fc` `--filter_drug` `drug_id`  
-Filter by drug ID, e.g. 'CHEMBL1743081'. *Only valid for the `pharmacogenetics` resource.*
-
-`-ft` `--filter_tissue` `tissue_id`  
-Filter by tissue ID, e.g. 'UBERON_0000473'. *Only valid for the `expression` and `depmap` resources.*
-
-`-fa` `--filter_anat_sys`  
-Filter by anatomical system, e.g. 'nervous system'. *Only valid for the `expression` resource.*
-
-`-fo` `--filter_organ` `anatomical_system`  
-Filter by organ, e.g. 'brain'. *Only valid for the `expression` resource.*
-
-`-fpa` `--filter_protein_a` `protein_a_id`  
-Filter by the protein ID of the first protein in the interaction, e.g. 'ENSP00000304915'. *Only valid for the `interactions` resource.*
-
-`-fpb` `--filter_protein_b` `protein_b_id`  
-Filter by the protein ID of the second protein in the interaction, e.g. 'ENSP00000379111'. *Only valid for the `interactions` resource.*
-
-`-fgb` `--filter_gene_b` `gene_b_id`  
-Filter by the gene ID of the second protein in the interaction, e.g. 'ENSG00000077238'. *Only valid for the `interactions` resource.*
-
-`filters`  
-Python only. A dictionary of filters, e.g.
-```python
-{'disease_id': ['EFO_0000274', 'HP_0000964']}
-```
-
-`filter_mode`  
-Python only. `filter_mode='or'` combines filters of different IDs with OR logic.
-`filter_mode='and'` combines filters of different IDs with AND logic (default).
+`--filters`  
+Filter results by exact equality using returned OpenTargets column names. Pass multiple filters by repeating the flag, e.g. '--filter disease.id=EFO_0000274 --filter drug.id=CHEMBL1743081'. Nested fields use dot notation, matching the column names returned by the API.
 
 **Flags**   
 `-csv` `--csv`  

docs/src/en/updates.md

@@ -6,6 +6,7 @@
   - some output column/key names may differ to reflect the new API structure
   - Removed the `--filter_mode` argument
 - [`gget blast`](blast.md): Fixed compatibility with newer pandas versions (≥ 2.0) where `pd.read_html()` no longer accepts raw HTML strings directly, causing a `FileNotFoundError` / `OSError: Filename too long` error when parsing BLAST results
+- [`gget cosmic`](cosmic.md): Added overwrite and gzip arguments to internals.
 
 **Version ≥ 0.30.3** (Feb 22, 2026):  
 - [`gget virus`](virus.md): New filtering options, quiet mode, and improved download reliability

gget/gget_cosmic.py

@@ -26,7 +26,7 @@ def is_valid_email(email):
     return re.match(email_pattern, email) is not None
 
 
-def download_reference(download_link, tar_folder_path, file_path, verbose, email = None, password = None):
+def download_reference(download_link, tar_folder_path, file_path, verbose, email = None, password = None, unzip = False):
     if not email:
         email = input("Please enter your COSMIC email: ")
     if not is_valid_email(email):
@@ -75,15 +75,16 @@ def download_reference(download_link, tar_folder_path, file_path, verbose, email
         if verbose:
             logger.info(f"Extracted tar file to {tar_folder_path}")
 
-    with gzip.open(f"{file_path}.gz", "rb") as f_in:
-        with open(file_path, "wb") as f_out:
-            shutil.copyfileobj(f_in, f_out)
-        if verbose:
-            logger.info(f"Unzipped file to {file_path}")
+    if unzip:
+        with gzip.open(f"{file_path}.gz", "rb") as f_in:
+            with open(file_path, "wb") as f_out:
+                shutil.copyfileobj(f_in, f_out)
+            if verbose:
+                logger.info(f"Unzipped file to {file_path}")
 
 
 def select_reference(
-    cosmic_project, reference_dir, grch_version, cosmic_version, verbose, email = None, password = None, overwrite = None
+    cosmic_project, reference_dir, grch_version, cosmic_version, verbose, email = None, password = None, unzip = True, overwrite = None
 ):
     # if cosmic_project == "transcriptome":
     #     download_link = f"https://cancer.sanger.ac.uk/api/mono/products/v1/downloads/scripted?path=grch{grch_version}/cosmic/v{cosmic_version}/Cosmic_Genes_Fasta_v{cosmic_version}_GRCh{grch_version}.tar&bucket=downloads"
@@ -149,6 +150,8 @@ def select_reference(
 
     tar_folder_path = os.path.join(reference_dir, tarred_folder)
     file_path = os.path.join(tar_folder_path, contained_file)
+    if not unzip:
+        file_path += ".gz"
 
     if os.path.exists(file_path):
         if overwrite is None:
@@ -195,7 +198,7 @@ def select_reference(
                 .lower()
             )
         if proceed in ["yes", "y"]:
-            download_reference(download_link, tar_folder_path, file_path, verbose, email = email, password = password)
+            download_reference(download_link, tar_folder_path, file_path, verbose, email = email, password = password, unzip = unzip)
         else:
             raise KeyboardInterrupt(
                 f"Database download canceled. Learn more about COSMIC at https://cancer.sanger.ac.uk/cosmic/download/cosmic."