diff options
Diffstat (limited to 'gn3/computations/rqtl.py')
| -rw-r--r-- | gn3/computations/rqtl.py | 45 |
1 files changed, 24 insertions, 21 deletions
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py index 7b1a35c..0433b3f 100644 --- a/gn3/computations/rqtl.py +++ b/gn3/computations/rqtl.py @@ -1,8 +1,9 @@ """Procedures related rqtl computations""" import os -import numpy as np from typing import Dict, List, Union +import numpy as np + from flask import current_app from gn3.commands import compose_rqtl_cmd @@ -54,27 +55,28 @@ def process_rqtl_output(file_name: str) -> List: marker_obs = [] # 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") as the_file: + with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"), + "output", file_name), "r") as the_file: for line in the_file: line_items = line.split(",") if line_items[1][1:-1] == "chr" or not line_items: # Skip header line continue - else: - # Convert chr to int if possible - the_chr: Union[int, str] - try: - the_chr = int(line_items[1][1:-1]) - except: - the_chr = line_items[1][1:-1] - this_marker = { - "name": line_items[0][1:-1], - "chr": the_chr, - "cM": float(line_items[2]), - "Mb": float(line_items[2]), - "lod_score": float(line_items[3]) - } - marker_obs.append(this_marker) + + # Convert chr to int if possible + the_chr: Union[int, str] + try: + the_chr = int(line_items[1][1:-1]) + except ValueError: + the_chr = line_items[1][1:-1] + this_marker = { + "name": line_items[0][1:-1], + "chr": the_chr, + "cM": float(line_items[2]), + "Mb": float(line_items[2]), + "lod_score": float(line_items[3]) + } + marker_obs.append(this_marker) return marker_obs @@ -85,14 +87,15 @@ def process_perm_output(file_name: str): """ perm_results = [] - with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"), "output", "PERM_" + file_name), "r") as the_file: + with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"), + "output", "PERM_" + file_name), "r") as the_file: for i, line in enumerate(the_file): if i == 0: # Skip header line continue - else: - line_items = line.split(",") - perm_results.append(float(line_items[1])) + + line_items = line.split(",") + perm_results.append(float(line_items[1])) suggestive = np.percentile(np.array(perm_results), 67) significant = np.percentile(np.array(perm_results), 95) |