diff options
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/rqtl.py | 40 |
1 files changed, 16 insertions, 24 deletions
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py index 8b1b316..b53efbd 100644 --- a/gn3/computations/rqtl.py +++ b/gn3/computations/rqtl.py @@ -11,7 +11,7 @@ from flask import current_app from gn3.commands import compose_rqtl_cmd from gn3.computations.gemma import generate_hash_of_string -from gn3.fs_helpers import get_hash_of_files, assert_path_exists +from gn3.fs_helpers import get_hash_of_files, assert_path_exists, get_tmpdir from gn3.debug import __pk__ @@ -68,13 +68,11 @@ 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] - with open( - os.path.join( - current_app.config.get("TMPDIR", "/tmp"), "output", file_name - ), - "r", - encoding="utf-8", - ) as the_file: + outdir = os.path.join(get_tmpdir(),"output") + 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: line_items = line.split(",") if line_items[1][1:-1] == "chr" or not line_items: @@ -115,13 +113,11 @@ def pairscan_for_figure(file_name: str) -> Dict: figure_data = {} # Open the file with the actual results, written as a list of lists - with open( - os.path.join( - current_app.config.get("TMPDIR", "/tmp"), "output", file_name - ), - "r", - encoding="utf8", - ) as the_file: + outdir = os.path.join(get_tmpdir(),"output") + 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 = [] for i, line in enumerate(the_file): if i == 0: # Skip first line @@ -322,15 +318,11 @@ def process_perm_output(file_name: str) -> Tuple[List, float, float]: suggestive and significant thresholds""" perm_results = [] - with open( - os.path.join( - current_app.config.get("TMPDIR", "/tmp"), - "output", - "PERM_" + file_name, - ), - "r", - encoding="utf-8", - ) as the_file: + outdir = os.path.join(get_tmpdir(),"output") + 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): if i == 0: # Skip header line |