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-rw-r--r--gn3/commands.py42
1 files changed, 42 insertions, 0 deletions
diff --git a/gn3/commands.py b/gn3/commands.py
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+++ b/gn3/commands.py
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+"""Procedures used to work with the various bio-informatics cli
+commands"""
+from typing import Dict
+from typing import List
+from typing import Optional
+
+from gn3.file_utils import lookup_file
+from gn3.file_utils import jsonfile_to_dict
+
+
+# pylint: disable=locally-disabled, too-many-arguments
+def compose_gemma_cmd(
+ token: str,
+ metadata_filename: str,
+ gemma_wrapper_cmd: str = "gemma-wrapper",
+ gemma_wrapper_kwargs: Optional[Dict] = None,
+ gemma_kwargs: Optional[Dict] = None,
+ gemma_args: Optional[List] = None) -> str:
+ """Compose a valid GEMMA command given the correct values"""
+ cmd = f"{gemma_wrapper_cmd} --json"
+ if gemma_wrapper_kwargs:
+ cmd += (" " # Add extra space between commands
+ " ".join([f" --{key} {val}" for key, val
+ in gemma_wrapper_kwargs.items()]))
+ data = jsonfile_to_dict(lookup_file("TMPDIR",
+ token,
+ metadata_filename))
+ geno_file = lookup_file(environ_var="TMPDIR",
+ root_dir="genotype",
+ file_name=data.get("geno", ""))
+ pheno_file = lookup_file(environ_var="TMPDIR",
+ root_dir=token,
+ file_name=data.get("geno", ""))
+ cmd += f" -- -g {geno_file} -p {pheno_file}"
+ if gemma_kwargs:
+ cmd += (" "
+ " ".join([f" -{key} {val}"
+ for key, val in gemma_kwargs.items()]))
+ if gemma_args:
+ cmd += (" "
+ " ".join([f" {arg}" for arg in gemma_args]))
+ return cmd