From d42b85ae5fcea1b71a7165fd6e64745a228c48f9 Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 18 Jun 2021 21:13:03 +0000 Subject: Fixed pylint issues --- gn3/api/rqtl.py | 7 ++++--- gn3/computations/rqtl.py | 45 ++++++++++++++++++++++++--------------------- 2 files changed, 28 insertions(+), 24 deletions(-) diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py index 38f4c1e..ebb746c 100644 --- a/gn3/api/rqtl.py +++ b/gn3/api/rqtl.py @@ -6,7 +6,6 @@ from flask import current_app from flask import jsonify from flask import request -from gn3.commands import run_cmd from gn3.computations.rqtl import generate_rqtl_cmd, process_rqtl_output, process_perm_output from gn3.computations.gemma import do_paths_exist @@ -45,13 +44,15 @@ run the rqtl_wrapper script and return the results as JSON ) rqtl_output = {} - if not os.path.isfile(os.path.join(current_app.config.get("TMPDIR"), "output", rqtl_cmd.get('output_file'))): + if not os.path.isfile(os.path.join(current_app.config.get("TMPDIR"), + "output", rqtl_cmd.get('output_file'))): os.system(rqtl_cmd.get('rqtl_cmd')) rqtl_output['results'] = process_rqtl_output(rqtl_cmd.get('output_file')) rqtl_output['results'] = process_rqtl_output(rqtl_cmd.get('output_file')) if int(rqtl_kwargs['nperm']) > 0: - rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'] = process_perm_output(rqtl_cmd.get('output_file')) + rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'] = \ + process_perm_output(rqtl_cmd.get('output_file')) return jsonify(rqtl_output) 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) -- cgit v1.2.3