From f887baaf66cc157f0c77237c41e70e42fe03549c Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 12 Feb 2021 16:36:21 +0300
Subject: Add new procedure for composing a gemma cmd

* gn3/commands.py: New file
* tests/unit/test_commands.py: New test-cases for ^^.
---
 gn3/commands.py | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 gn3/commands.py

(limited to 'gn3')

diff --git a/gn3/commands.py b/gn3/commands.py
new file mode 100644
index 0000000..50b6d29
--- /dev/null
+++ b/gn3/commands.py
@@ -0,0 +1,42 @@
+"""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
-- 
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