Add files via upload

Author: Brycealong

get_path.py

@@ -0,0 +1,24 @@
+import sys
+import os
+
+
+def resource_path(relative_path, parent_path=False):
+    '''返回资源绝对路径。'''
+    if hasattr(sys, '_MEIPASS'):
+        # PyInstaller会创建临时文件夹temp
+        # 并把路径存储在_MEIPASS中
+        base_path = sys._MEIPASS
+    else:
+        base_path = os.path.abspath('.')
+    if not parent_path:
+        return os.path.join(base_path, relative_path)
+    else:
+        return os.path.abspath(os.path.join(base_path, relative_path, ".."))
+
+
+def make_dirs():
+    dirs = ["Excel_Files", "None_Pretreated_Files", "Pretreated_Files"]
+    root_path = resource_path("", True)
+    for dir in dirs:
+        if not os.path.exists(os.path.join(root_path, dir)):
+            os.mkdir(os.path.join(root_path, dir))

main.py

@@ -0,0 +1,108 @@
+import argparse
+import os
+import sys
+
+from functions.vcf_handle import VCF2Excel
+from functions.pretreatment import Pretreatment
+from functions.none_pretreatment import NonePretreatment
+from functions.Statistic_Methods import Statistic
+
+
+def main(args):
+    if args.p == 1:
+        args.p = True
+    else:
+        args.p = False
+
+    if args.p2 == 1:
+        args.p2 = True
+    else:
+        args.p2 = False
+
+    if args.p3 == 1:
+        args.p3 = True
+    else:
+        args.p3 = False
+    print("-" * 100)
+    print(
+        "file path:{}\nmethod:{}\nis pretreatment:{}\nread number:{}\nChi-square test:{}\nContinuity test:{}\nsmooth method:{}\nsmooth window size:{}\nthreshold:{}".format(
+            args.i, args.m, args.p, args.p1, args.p2, args.p3, args.s, args.w, args.t))
+    print("-" * 100)
+    # 新建文件夹
+    root_path = os.getcwd()
+    pretreatment_dir = os.path.join(root_path, "Pretreated_Files")
+    nopretreatment_dir = os.path.join(root_path, "NoPretreatment")
+    excel_path = os.path.join(root_path, "Excel_Files")
+    # filtered_vcf_dir = os.path.join(root_path, "Filtered_VCFs")
+    for path in [pretreatment_dir, nopretreatment_dir, excel_path]:
+        if not os.path.exists(path):
+            os.mkdir(path)
+    # 获得文件名、类型
+    temp = args.i.split("/")[-1]
+    file_name = temp.split(".")[0]
+    file_type = temp.split(".")[1]
+
+    if "vcf" in file_type:
+        vcf2excel = VCF2Excel(args.i, file_name, excel_path, args.chromosomes, args.samples)
+        file_path = vcf2excel.run()
+    else:
+        file_path = args.i
+
+    if args.p:
+        return_path = os.path.exists(os.path.join(pretreatment_dir, file_name + "_{}".format(args.p1) + "_freq.npy"))
+        pretreat = Pretreatment(args.p1, args.p2, args.p3, file_path, file_name, pretreatment_dir)
+        ref_data_path, mut_data_path, freq_data_path, pos_data_path, chrome_set = pretreat.run(return_path)
+        if not return_path:
+            print("pretreatment & files do not exist")
+        else:
+            print("pretreatment & files exist")
+    else:
+        return_path = os.path.exists(os.path.join(nopretreatment_dir, file_name + "_ref.npy"))
+        nopretreat = NonePretreatment(file_path, file_name, nopretreatment_dir)
+        ref_data_path, mut_data_path, freq_data_path, pos_data_path, chrome_set = nopretreat.run(return_path)
+        if not return_path:
+            print("nonepretreatment & files do not exist")
+        else:
+            print("nonepretreatment & files exist")
+    # print("chromosome list: ", chrome_set)
+    rsp = os.path.join(os.getcwd(), "Results")
+    if not os.path.exists(rsp):
+        os.mkdir(rsp)
+    save_path = os.path.join(rsp, file_name)
+    if not os.path.exists(save_path):
+        os.mkdir(save_path)
+    for m in args.m:
+        dl = Statistic(m, freq_data_path, ref_data_path, mut_data_path,
+                       pos_data_path, chrome_set, args.p1, args.s,
+                       args.w, args.t, save_path)
+        dl.run()
+
+
+# example:
+# python main.py --i /media/xaun/CXX/DeepBSA-terminal/bin/Excel_Files/nc-planthigh-pop1.csv --p False
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    # 载入数据及预处理
+    parser.add_argument("--i", default=None, required=True, type=str, help="The input file path(vcf/csv).")
+    parser.add_argument("--m", default=["DL"], nargs='+', type=str,
+                        help="List of algorithms to use(DL/K/ED4/SNP/SmoothG/SmoothLOD/Ridit) used. Default is DL.")
+    parser.add_argument("--p", default=1, type=int,
+                        help="Whether to pretreatment data(1[True] or 0[False]). Default is True.")
+    parser.add_argument("--p1", default=0, type=int,
+                        help="Pretreatment step 1: Number of read thread, the SNP whose number lower than it will be filtered. Default is 0.")
+    parser.add_argument("--p2", default=1, type=int,
+                        help="Pretreatment step 2: Chi-square test(1[True] or 0[False]). Default is 1[True].")
+    parser.add_argument("--p3", default=1, type=int,
+                        help="Pretreatment step 3: Continuity test(1[True] or 0[False]). Default is 1[True].")
+    parser.add_argument("--chromosomes", default=[], nargs='+', type=str, help="List of chromosomes to select.")
+    parser.add_argument("--samples", default=[], nargs='+', type=str, help="List of samples to select.")
+    # 方法选择等
+    parser.add_argument("--s", default="LOWESS", type=str,
+                        help="The function to smooth the result(Tri-kernel-smooth/LOWESS/Moving Average), Defalut is LOWESS")
+    parser.add_argument("--w", default=0, type=float,
+                        help="Windows size of LOESS. The number is range from 0-1. 0 presents the best size for minimum AICc. Default is 0(auto).")
+    parser.add_argument("--t", default=0, type=float, help="The threshold to find peaks(float). Default is 0(auto)")
+
+    args = parser.parse_args()
+
+    main(args)