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authorPjotr Prins2024-04-03 13:31:43 +0200
committerFrederick Muriuki Muriithi2024-09-12 07:42:03 -0500
commitde5a77cb18401c761760a0dc4af6104c0b2be9dd (patch)
tree2fc2485833973cbc06353f9549aed4c83c62be73 /gn3/computations
parent4dd2ab8da310a34e598553ef951d3233ded9d1ab (diff)
downloadgenenetwork3-de5a77cb18401c761760a0dc4af6104c0b2be9dd.tar.gz
From gn3 only use TMPDIR/gn3 paths
Diffstat (limited to 'gn3/computations')
-rw-r--r--gn3/computations/gemma.py13
-rw-r--r--gn3/computations/rqtl.py6
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):