fix ref panel upper case

src/baskerville/helpers/gcs_utils.py

@@ -1,3 +1,7 @@
+# taken and modified from calico-ukbb-mri-ml repo
+# https://github.com/calico/calicolabs-ukbb-mri-ml/tree/main/src/ukbb_mri_ml/helpers
+# =========================================================================
+
 import os
 import logging
 
@@ -11,29 +15,36 @@
 from google.auth.exceptions import DefaultCredentialsError
 
 logger = logging.getLogger(__name__)
-PREFIX = ""
 
 logger = logging.getLogger(__name__)
 
-try:
-    # Attempt to infer credentials from environment
-    storage_client = Client()
-    logger.info("Inferred credentials from environment")
-except DefaultCredentialsError:
+
+def _get_storage_client() -> Client:
+    """
+    Returns: Google Cloud Storage Client
+    """
     try:
-        # Attempt to load JSON credentials from GOOGLE_APPLICATION_CREDENTIALS
-        storage_client = Client.from_service_account_info(
-            os.environ["GOOGLE_APPLICATION_CREDENTIALS"]
-        )
-        logger.info("Loaded credentials from GOOGLE_APPLICATION_CREDENTIALS")
-    except AttributeError:
-        # Attempt to load JSON credentials from base64 encoded string
-        storage_client = Client.from_service_account_info(
-            loads(
-                b64decode(os.environ["GOOGLE_APPLICATION_CREDENTIALS"]).decode("utf-8")
+        # Attempt to infer credentials from environment
+        storage_client = Client()
+        logger.info("Inferred credentials from environment")
+    except DefaultCredentialsError:
+        try:
+            # Attempt to load JSON credentials from GOOGLE_APPLICATION_CREDENTIALS
+            storage_client = Client.from_service_account_info(
+                os.environ["GOOGLE_APPLICATION_CREDENTIALS"]
             )
-        )
-        logger.info("Loaded credentials from base64 encoded string")
+            logger.info("Loaded credentials from GOOGLE_APPLICATION_CREDENTIALS")
+        except AttributeError:
+            # Attempt to load JSON credentials from base64 encoded string
+            storage_client = Client.from_service_account_info(
+                loads(
+                    b64decode(os.environ["GOOGLE_APPLICATION_CREDENTIALS"]).decode(
+                        "utf-8"
+                    )
+                )
+            )
+            logger.info("Loaded credentials from base64 encoded string")
+    return storage_client
 
 
 def download_from_gcs(gcs_path: str, local_path: str, bytes=True) -> None:
@@ -47,6 +58,7 @@ def download_from_gcs(gcs_path: str, local_path: str, bytes=True) -> None:
     Returns: None
 
     """
+    storage_client = _get_storage_client()
     write_mode = "wb" if bytes else "w"
     with open(local_path, write_mode) as o:
         storage_client.download_blob_to_file(gcs_path, o)
@@ -66,6 +78,7 @@ def sync_dir_to_gcs(
     Returns: None
 
     """
+    storage_client = _get_storage_client()
     if not is_gcs_path(gcs_dir):
         raise ValueError(f"gcs_dir is not a valid GCS path: {gcs_dir}")
 
@@ -105,6 +118,7 @@ def upload_folder_gcs(local_dir: str, gcs_dir: str) -> None:
         gcs_dir: string GCS destination path. Will create folders that do not exist.
     Returns: None
     """
+    storage_client = _get_storage_client()
     bucket_name = gcs_dir.split("//")[1].split("/")[0]
     gcs_object_prefix = gcs_dir.split("//")[1].split("/")[1]
     local_prefix = local_dir.split("/")[-1]
@@ -116,6 +130,24 @@ def upload_folder_gcs(local_dir: str, gcs_dir: str) -> None:
         blob.upload_from_filename(local_file)
 
 
+def upload_file_gcs(local_path: str, gcs_path: str, bytes=True) -> None:
+    """
+    Upload a file to gcs
+    Args:
+        local_path: local path to file
+        gcs_path: string GCS Uri follows the format gs://$BUCKET_NAME/OBJECT_NAME
+
+    Returns: None
+    """
+    storage_client = _get_storage_client()
+    bucket_name = gcs_path.split("//")[1].split("/")[0]
+    bucket = storage_client.bucket(bucket_name)
+    gcs_object_prefix = gcs_path.split("//")[1].split("/")[1]
+    filename = local_path.split("/")[-1]
+    blob = bucket.blob(f"{gcs_object_prefix}/{filename}")
+    blob.upload_from_filename(local_path)
+
+
 def gcs_join(*args):
     args = [arg.replace("gs://", "").strip("/") for arg in args]
     return "gs://" + join(*args)
@@ -156,34 +188,45 @@ def get_filename_in_dir(files_dir: str, recursive: bool = False) -> List[str]:
     """
     # currently only Niftidataset receives gs bucket paths, so this isn't necessary
     # commenting out for now even though it is functional (lots of files)
+    storage_client = _get_storage_client()
     if is_gcs_path(files_dir):
         bucket_name, object_name = split_gcs_uri(files_dir)
         blob_iterator = storage_client.list_blobs(bucket_name, prefix=object_name)
-        # return [str(blob) for blob in blob_iterator if "/" not in blob.name]
         return [str(blob) for blob in blob_iterator]
-    else:
-        dir_contents = os.listdir(files_dir)
-        files = []
-        for entry in dir_contents:
-            entry_path = join(files_dir, entry)
-            if isfile(entry_path):
-                files.append(entry_path)
-            elif recursive:
-                files.extend(get_filename_in_dir(entry_path, recursive=recursive))
-            else:
-                pass
-        return files
+    dir_contents = os.listdir(files_dir)
+    files = []
+    for entry in dir_contents:
+        entry_path = join(files_dir, entry)
+        if isfile(entry_path):
+            files.append(entry_path)
+        elif recursive:
+            files.extend(get_filename_in_dir(entry_path, recursive=recursive))
+        else:
+            print("Nothing happened here")
+            pass
+    return files
 
 
-def download_rename_inputs(filepath: str, temp_dir: str):
+def download_rename_inputs(filepath: str, temp_dir: str) -> str:
     """
     Download file from gcs to local dir
     Args:
         filepath: GCS Uri follows the format gs://$BUCKET_NAME/OBJECT_NAME
     Returns: new filepath in the local machine
     """
     _, filename = split_gcs_uri(filepath)
-    if "/" in filename:
-        filename = filename.split("/")[-1]
     download_from_gcs(filepath, f"{temp_dir}/{filename}")
     return f"{temp_dir}/{filename}"
+
+
+def gcs_file_exist(gcs_path: str) -> bool:
+    """
+    check if a file exist in gcs
+    params: gcs_path
+    returns: true/false
+    """
+    storage_client = _get_storage_client()
+    bucket, filename = split_gcs_uri(gcs_path)
+    bucket = storage_client.bucket(bucket)
+    blob = bucket.blob(filename)
+    return blob.exists()

src/baskerville/vcf.py

@@ -599,8 +599,7 @@ def vcf_snps(
             if validate_ref_fasta is not None:
                 ref_n = len(snps[-1].ref_allele)
                 snp_pos = snps[-1].pos - 1
-                ref_snp = genome_open.fetch(snps[-1].chr, snp_pos, snp_pos + ref_n)
-
+                ref_snp = genome_open.fetch(snps[-1].chr, snp_pos, snp_pos + ref_n).upper()
                 if snps[-1].ref_allele != ref_snp:
                     if not flip_ref:
                         # bail