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-rw-r--r--gn3/computations/rqtl.py50
1 files changed, 25 insertions, 25 deletions
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 087a99f..0e8cd1f 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -1,25 +1,25 @@
-"""Procedures related rqtl computations"""
-import os
-
-from typing import Dict
-from gn3.commands import compose_rqtl_cmd
-from gn3.fs_helpers import get_hash_of_files
-
-def generate_rqtl_cmd(rqtl_wrapper_cmd: str,
- output_dir: str,
- rqtl_wrapper_kwargs: Dict) -> Dict:
-
- _hash = get_hash_of_files(
- [v for k, v in rqtl_wrapper_kwargs.items() if k in ["g", "p", "addcovar",
- "model", "method",
- "interval", "nperm",
- "scale", "control"]])
-
- _output_filename = f"{_hash}-output.json"
- return {
- "output_file":
- _output_filename,
- "rqtl_cmd":
- compose_rqtl_cmd(rqtl_wrapper_cmd=rqtl_wrapper_cmd,
- rqtl_wrapper_kwargs=rqtl_wrapper_kwargs)
- } \ No newline at end of file
+"""Procedures related rqtl computations"""
+
+from typing import Dict
+from gn3.commands import compose_rqtl_cmd
+from gn3.fs_helpers import get_hash_of_files
+
+def generate_rqtl_cmd(rqtl_wrapper_cmd: str,
+ rqtl_wrapper_kwargs: Dict) -> Dict:
+ """Given the base rqtl_wrapper command and
+dict of keyword arguments, return the full rqtl_wrapper command and an
+output filename generated from a hash of the genotype and phenotype files
+
+ """
+
+ _hash = get_hash_of_files(
+ [v for k, v in rqtl_wrapper_kwargs.items() if k in ["g", "p"]])
+
+ _output_filename = f"{_hash}-output.json"
+ return {
+ "output_file":
+ _output_filename,
+ "rqtl_cmd":
+ compose_rqtl_cmd(rqtl_wrapper_cmd=rqtl_wrapper_cmd,
+ rqtl_wrapper_kwargs=rqtl_wrapper_kwargs)
+ }