Changeset 1021 for framspy

Timestamp:

07/28/20 16:00:06 (4 years ago)

Author:

Maciej Komosinski

Message:

Checking for genotype validity can now handle multiple genotypes at once

File:

• framspy/FramsticksCLI.py (modified) (5 diffs)

framspy/FramsticksCLI.py

@@ -38 +38 @@
         DISSIMIL_CMD = "dissimil"
         DISSIMIL_FILE = "dissimilarity_matrix.tsv"  # tab-separated values
-        ISVALID_CMD = "isvalid"
+        ISVALID_CMD = "arevalid"
         ISVALID_FILE = "validity.txt"
         MUTATE_CMD = "mutate"
@@ -90 +90 @@
 
                 self.__readFromFramsCLIUntil("UserScripts.autoload")
-                print('Performing a basic test 1/3... ', end='')
+                print('Performing a basic test 1/2... ', end='')
                 assert self.getSimplest("1") == "X"
                 print('OK.')
-                print('Performing a basic test 2/3... ', end='')
-                assert self.isValid("X[0:0]") is True
-                print('OK.')
-                print('Performing a basic test 3/3... ', end='')
-                assert self.isValid("X[0:0],") is False
+                print('Performing a basic test 2/2... ', end='')
+                assert self.isValid(["X[0:0],", "X[0:0]", "X[1:0]"]) == [False, True, False]
                 print('OK.')
                 if not self.DETERMINISTIC:
@@ -249 +246 @@
                         A square array with dissimilarities of each pair of genotypes.
                 """
+                assert isinstance(genotype_list, list)  # because in python str has similar capabilities as list and here it would pretend to work too, so to avoid any ambiguity
                 files = self.__runCommand(self.DISSIMIL_CMD, genotype_list, self.DISSIMIL_FILE, self.GENO_SAVE_FILE_FORMAT["NATIVEFRAMS"])
                 with open(files[-1]) as f:
@@ -265 +263 @@
 
 
-        def isValid(self, genotype: str) -> bool:
-                files = self.__runCommand(self.ISVALID_CMD, [genotype], self.ISVALID_FILE, self.GENO_SAVE_FILE_FORMAT["RAWGENO"])
-                with open(files[-1]) as f:
-                        valid = f.readline() == "1"
-                self.__cleanUpCommandResults(files)
+        def isValid(self, genotype_list: List[str]) -> List[bool]:
+                assert isinstance(genotype_list, list)  # because in python str has similar capabilities as list and here it would pretend to work too, so to avoid any ambiguity
+                files = self.__runCommand(self.ISVALID_CMD, genotype_list, self.ISVALID_FILE, self.GENO_SAVE_FILE_FORMAT["NATIVEFRAMS"])
+                valid = []
+                with open(files[-1]) as f:
+                        for line in f:
+                                valid.append(line.strip() == "1")
+                self.__cleanUpCommandResults(files)
+                assert len(genotype_list) == len(valid), "Submitted %d genotypes, received %d validity values" % (len(genotype_list), len(valid))
                 return valid
 
@@ -319 +321 @@
         print('\tDissimilarity of Parent1 and Offspring:', framsCLI.dissimilarity([parent1, offspring])[0, 1])
         print('\tPerformance of Offspring:', framsCLI.evaluate(offspring))
-        print('\tValidity of Offspring:', framsCLI.isValid(offspring))
+        print('\tValidity of Parent1, Parent 2, and Offspring:', framsCLI.isValid([parent1, parent2, offspring]))
 
         framsCLI.closeFramsticksCLI()