tools

chart/tools.py

@@ -3,6 +3,8 @@ import random
 import time
 
 import pandas as pd
+from Bio import SeqIO
+from Bio.SeqUtils import GC
 
 from Simple_Drawing.settings import BASE_DIR
 
@@ -338,7 +340,7 @@ class="layui-input" style="height: 25px; width:80px;margin-top: 6px">
             for d in self.Basics[title]:
                 parameter = ChartParameter(d)
 
-                if parameter.input_type in ["rgb","hex",'color_name']:
+                if parameter.input_type in ["rgb", "hex", 'color_name']:
                     code += f"""{parameter.name}:{parameter.name},
 """
                 else:
@@ -349,7 +351,7 @@ class="layui-input" style="height: 25px; width:80px;margin-top: 6px">
             for d in self.Senior[title]:
                 parameter = ChartParameter(d)
                 print(parameter.input_type)
-                if parameter.input_type in ["rgb", "hex",'color_name']:
+                if parameter.input_type in ["rgb", "hex", 'color_name']:
                     code += f"""{parameter.name}:{parameter.name},
                 """
                 else:
@@ -381,7 +383,7 @@ class="layui-input" style="height: 25px; width:80px;margin-top: 6px">
             }
         });
         })
-            """ % (i, random_color(), fl,i)
+            """ % (i, random_color(), fl, i)
 
         return code
 
@@ -404,4 +406,68 @@ Treemap = {
 }
 
 
+class Basics(object):
+    def __init__(self, file_path, args):
+        self.args = args
+        self.file_path = file_path
+        self.out_file = []
+        self.f = SeqIO.parse(file_path, "fasta")  # 读取多条序列
 
+    def Sequence_cleaning(self):
+        f = self.f
+        temp = []
+        for i in f:
+            temp.append(f">{i.id}\n{str(i.seq)}")
+        self.out_file.append(["Sequence_cleaning", temp])
+
+    def Sequence_length(self):
+        f = self.f
+        temp = []
+        for i in f:
+            temp.append(f"{i.id}\t{len(i)}")
+        self.out_file.append(["Sequence_length", temp])
+
+    def GC_content(self):
+        f = self.f
+        temp = []
+        for i in f:
+            CONTENT = GC(str(i.seq))
+            temp.append(f"{i.id}\t{CONTENT}")
+        self.out_file.append(["GC_content", temp])
+
+    def Sequence_flip(self):
+        f = self.f
+        temp = []
+        for i in f:
+            temp.append(f">{i.id}\n{str(i.reverse_complement().seq)}")
+        self.out_file.append(["Sequence_flip", temp])
+
+    def Reverse_complementarity(self):
+        f = self.f
+        temp = []
+        for i in f:
+            temp.append(f">{i.id}\n{str(i.complement().seq)}")
+        self.out_file.append(["Reverse_complementarity", temp])
+
+    # def Codon_preference(self):
+    #     f = self.f
+    #     temp = []
+    #     for i in f:
+    #         temp.append(f">{i.id}\n{str(i.complement().seq)}")
+    #     self.out_file.append({"Reverse_complementarity": temp})
+
+    def run(self):
+        for i in self.args.keys():
+            if self.args[i] == "YES":
+                eval(f"self.{self.args[i]}")()
+
+        data = ""
+        for i in self.out_file:
+            for j in i:
+                data += f"\n{'-' * 15}\n{j[0]}\n"
+                data += "\n".join(i[1])
+
+        with open(self.file_path, "w") as f:
+            f.write(data)
+
+        return data