From de5a77cb18401c761760a0dc4af6104c0b2be9dd Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 3 Apr 2024 13:31:43 +0200
Subject: From gn3 only use TMPDIR/gn3 paths

---
 gn3/computations/gemma.py | 13 +++++++------
 gn3/computations/rqtl.py  |  6 ------
 2 files changed, 7 insertions(+), 12 deletions(-)

diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
index 2c367ff..577d8e8 100644
--- a/gn3/computations/gemma.py
+++ b/gn3/computations/gemma.py
@@ -22,23 +22,24 @@ def generate_pheno_txt_file(trait_filename: str,
                             values: List,
                             tmpdir: str = "/tmp") -> str:
     """Given VALUES, and TMPDIR, generate a valid traits file"""
-    if not os.path.isdir(f"{tmpdir}/gn2/"):
-        os.mkdir(f"{tmpdir}/gn2/")
+
+    if not os.path.isdir(f"{tmpdir}/gn3/"):
+        os.mkdir(f"{tmpdir}/gn3/")
     ext = trait_filename.partition(".")[-1]
     if ext:
         trait_filename = trait_filename.replace(f".{ext}", "")
         ext = f".{ext}"
     trait_filename += f"_{generate_hash_of_string(''.join(values))}{ext}"
     # Early return if this already exists!
-    if os.path.isfile(f"{tmpdir}/gn2/{trait_filename}"):
-        return f"{tmpdir}/gn2/{trait_filename}"
-    with open(f"{tmpdir}/gn2/{trait_filename}", "w", encoding="utf-8") as _file:
+    if os.path.isfile(f"{tmpdir}/gn3/{trait_filename}"):
+        return f"{tmpdir}/gn3/{trait_filename}"
+    with open(f"{tmpdir}/gn3/{trait_filename}", "w", encoding="utf-8") as _file:
         for value in values:
             if value == "x":
                 _file.write("NA\n")
             else:
                 _file.write(f"{value}\n")
-    return f"{tmpdir}/gn2/{trait_filename}"
+    return f"{tmpdir}/gn3/{trait_filename}"
 
 
 # pylint: disable=R0913
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 589caa4..0b8c23d 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -69,8 +69,6 @@ def process_rqtl_mapping(file_name: str) -> List:
     # Later I should probably redo this using csv.read to avoid the
     # awkwardness with removing quotes with [1:-1]
     outdir = os.path.join(get_tmpdir(),"gn3")
-    if not os.path.isdir(outdir):
-        os.mkdir(outdir)
 
     with open( os.path.join(outdir,file_name),"r",encoding="utf-8") as the_file:
         for line in the_file:
@@ -114,8 +112,6 @@ def pairscan_for_figure(file_name: str) -> Dict:
 
     # Open the file with the actual results, written as a list of lists
     outdir = os.path.join(get_tmpdir(),"gn3")
-    if not os.path.isdir(outdir):
-        os.mkdir(outdir)
 
     with open( os.path.join(outdir,file_name),"r",encoding="utf-8") as the_file:
         lod_results = []
@@ -319,8 +315,6 @@ def process_perm_output(file_name: str) -> Tuple[List, float, float]:
 
     perm_results = []
     outdir = os.path.join(get_tmpdir(),"gn3")
-    if not os.path.isdir(outdir):
-        os.mkdir(outdir)
 
     with open( os.path.join(outdir,file_name),"r",encoding="utf-8") as the_file:
         for i, line in enumerate(the_file):
-- 
cgit v1.2.3