{"action":"created","comment":{"url":"https://api.github.com/repos/parseq/digital-phenotyping/pulls/comments/72940038","id":72940038,"diff_hunk":"@@ -0,0 +1,314 @@\n+#!/usr/bin/env python3\n+# -*- coding: utf-8 -*-\n+\n+import argparse\n+import sys\n+import os\n+import re\n+import csv\n+import numpy as np\n+import pandas as pd\n+import math\n+import ast\n+\n+\n+# Print all the arguments given to the program\n+def check_arg(args=None):\n+    parser = argparse.ArgumentParser(description='Choose analysis mode and input data')\n+    parser.add_argument('-m', '--mode',\n+                        help='mode of analysis: eye, hair, skin',\n+                        required='True',\n+                        default='total')\n+    parser.add_argument('-v', '--vcf',\n+                        help='genotyping data path',\n+                        required='True')\n+    parser.add_argument('-p', '--param',\n+                        help='parameters data path, (default: self-report/ directory in repo)',\n+                        default='self-report/')\n+    parser.add_argument('-s', '--silent',\n+                        help='on / off -- print the output or not',\n+                        default='on')\n+    results = parser.parse_args()\n+\n+    return (results.mode,\n+            results.vcf,\n+            results.param,\n+            results.silent)\n+\n+\n+# Get the list rs relevant for particular mode of the analysis\n+def get_rs(mode, path_to_param):\n+    if path_to_param != 'self-report/':\n+        usepath = path_to_param\n+    else:\n+        usepath = os.path.abspath('self-report/')\n+    rsnp = []\n+    for file in os.listdir(usepath):\n+        # select eye / hair / skin -marks.txt\n+        if file.startswith(mode):\n+            address = os.path.abspath(os.path.join(usepath, file))\n+            with open(address, 'r', encoding='cp1252') as f:\n+                for line in f:\n+                    # exclude comment lines\n+                    if line and not line.startswith('#'):\n+                        line = str.strip(line)\n+                        rsnp.append(line)\n+\n+    return rsnp\n+\n+\n+def 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полезно внести правки, аналогичные сделанным в функции 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