Add option for output rounding digits #271

Author: XingerTang

docs/source/usage.rst

@@ -196,7 +196,11 @@ Output options
       -out_id_only          Suppress output for individuals not present in
                             the file specified with -out_id_order. It also suppresses
                             "dummy" individuals.
-
+      -out_digits           Specify the number of digits to round the outputs. 
+                            Does not apply to outputs from ``alt_allele_prob``, 
+                            ``geno_error_prob``, ``seq_error_prob``, 
+                            and ``pheno_penetrance``. 
+                            Default: 4.
 |Software| by default produces a :ref:`dosage file <dosage_file_format>`.
 Additional individual-level outputs can be requested with the options described above.
 

pyproject.toml

@@ -22,6 +22,7 @@ dependencies = [
     "numpy>=1.19",
     "numba>=0.50.0"
 ]
+requires-python = ">= 3.6"
 
 [project.scripts]
 # correspond to entry_points

src/tinypeel/Peeling/PeelingIO.py

@@ -92,18 +92,20 @@ def writeOutParamaters(peelingInfo):
     :return: None. Writes to files specified in the InputOutput.args.
     """
     args = InputOutput.args
-
     if args.est_geno_error_prob:
         np.savetxt(
-            args.out_file + ".geno_error_prob.txt", peelingInfo.genoError, fmt="%f"
+            args.out_file + ".geno_error_prob.txt",
+            peelingInfo.genoError,
         )
     if args.est_seq_error_prob:
         np.savetxt(
-            args.out_file + ".seq_error_prob.txt", peelingInfo.seqError, fmt="%f"
+            args.out_file + ".seq_error_prob.txt",
+            peelingInfo.seqError,
         )
     if args.rec_prob:
         np.savetxt(
-            args.out_file + ".rec_prob.txt", np.empty((1, 1)), fmt="%f"
+            args.out_file + ".rec_prob.txt",
+            np.empty((1, 1)),
         )  # not implemented atm, just as a placeholder
     # np.savetxt(args.out_file + ".trans", peelingInfo.transmissionRate, fmt = "%f")
 
@@ -134,7 +136,6 @@ def sort_key(mf_key):
         args.out_file + ".alt_allele_prob.txt",
         combined_AAP,
         delimiter="\t",
-        fmt="%.2f",
         header="\t".join(sorted_MF),
         comments="",
     )
@@ -149,7 +150,8 @@ def writePhenoPenetrance(pedigree):
     """
     args = InputOutput.args
     np.savetxt(
-        args.out_file + ".pheno_penetrance.txt", pedigree.phenoPenetrance, fmt="%.2f"
+        args.out_file + ".pheno_penetrance.txt",
+        pedigree.phenoPenetrance,
     )
 
 
@@ -249,13 +251,17 @@ def writePhasedGenoProbs(pedigree, genoProbFunc, outputFile):
     :type outputFile: str
     :return: None. Writes to the specified output file.
     """
+    args = InputOutput.args
     with open(outputFile, "w+") as f:
         for idx, ind in pedigree.writeOrder():
             matrix = genoProbFunc(ind.idn, ind.sex)
             f.write("\n")
             for i in range(matrix.shape[0]):
                 f.write(
-                    ind.idx + " " + " ".join(map("{:.4f}".format, matrix[i, :])) + "\n"
+                    ind.idx
+                    + " "
+                    + " ".join(map(f"{{:.{args.out_digits}f}}".format, matrix[i, :]))
+                    + "\n"
                 )
 
 
@@ -270,6 +276,7 @@ def writeGenoProbs(pedigree, genoProbFunc, outputFile):
     :type outputFile: str
     :return: None. Writes to the specified output file.
     """
+    args = InputOutput.args
     with open(outputFile, "w+") as f:
         for idx, ind in pedigree.writeOrder():
             matrix = genoProbFunc(ind.idn, ind.sex)
@@ -279,15 +286,20 @@ def writeGenoProbs(pedigree, genoProbFunc, outputFile):
                         ind.idx
                         + " "
                         + " ".join(
-                            map("{:.4f}".format, matrix[i, :] + matrix[i + 1, :])
+                            map(
+                                f"{{:.{args.out_digits}f}}".format,
+                                matrix[i, :] + matrix[i + 1, :],
+                            )
                         )
                         + "\n"
                     )
                 elif i != 2:  # Print probabilities for aa and AA
                     f.write(
                         ind.idx
                         + " "
-                        + " ".join(map("{:.4f}".format, matrix[i, :]))
+                        + " ".join(
+                            map(f"{{:.{args.out_digits}f}}".format, matrix[i, :])
+                        )
                         + "\n"
                     )
 
@@ -308,7 +320,10 @@ def writePhenoProbs(pedigree, phenoProbFunc):
             f.write("\n")
             for i in range(matrix.shape[0]):
                 f.write(
-                    ind.idx + " " + " ".join(map("{:.4f}".format, matrix[i, :])) + "\n"
+                    ind.idx
+                    + " "
+                    + " ".join(map(f"{{:.{args.out_digits}f}}".format, matrix[i, :]))
+                    + "\n"
                 )
 
 
@@ -325,14 +340,20 @@ def writeDosages(pedigree, genoProbFunc, isXChr, outputFile):
     :type outputFile: str
     :return: None. Writes to the specified output file.
     """
+    args = InputOutput.args
     with open(outputFile, "w+") as f:
         for idx, ind in pedigree.writeOrder():
             if isXChr and ind.sex == 0:
                 tmp = np.array([0, 0, 0, 1])
             else:
                 tmp = np.array([0, 1, 1, 2])
             matrix = np.dot(tmp, genoProbFunc(ind.idn, ind.sex))
-            f.write(ind.idx + " " + " ".join(map("{:.4f}".format, matrix)) + "\n")
+            f.write(
+                ind.idx
+                + " "
+                + " ".join(map(f"{{:.{args.out_digits}f}}".format, matrix))
+                + "\n"
+            )
 
 
 def writeCalledGenotypes(pedigree, genoProbFunc, isXChr, outputFile, thresh):

src/tinypeel/tinypeel.py

@@ -545,6 +545,13 @@ def get_output_options():
         required=False,
         help='Suppress output for individuals not present in the file specified with -out_id_order. It also suppresses "dummy" individuals.',
     )
+    parse_dictionary["out_digits"] = lambda parser: parser.add_argument(
+        "-out_digits",
+        default=4,
+        type=int,
+        required=False,
+        help="Specify the number of digits to round the outputs. Does not apply to outputs from ``alt_allele_prob``, ``geno_error_prob``, ``seq_error_prob``, and ``pheno_penetrance``. Default: 4.",
+    )
 
     return parse_dictionary
 
@@ -712,7 +719,7 @@ def getArgs():
     InputOutput.add_arguments_from_dictionary(
         output_parser,
         get_output_options(),
-        options=["writekey", "onlykeyed"],
+        options=["writekey", "onlykeyed", "out_digits"],
     )
 
     # Multithreading

tests/functional_tests/run_func_test.py

@@ -695,7 +695,7 @@ def test_alt_allele_prob(self):
 
         self.input_files = ["geno_file", "ped_file"]
         self.input_file_depend_on_test_cases = self.input_files
-        self.arguments = {"method": "multi", "out_id_only": None}
+        self.arguments = {"method": "multi", "out_id_only": None, "out_digits": 2}
 
         for self.test_cases in [
             "default",

tests/functional_tests/test_alt_allele_prob/true-alt_allele_prob-both.txt

@@ -1,6 +1,6 @@
 MF_1
-0.50
-0.50
-0.50
-0.50
-0.50
+5.000000000000000000e-01
+5.000000000000000000e-01
+5.000000000000000000e-01
+5.000000000000000000e-01
+5.000000000000000000e-01

tests/functional_tests/test_alt_allele_prob/true-alt_allele_prob-default.txt

@@ -1,6 +1,6 @@
 MF_1	MF_2
-0.50	0.50
-0.50	0.50
-0.50	0.50
-0.50	0.50
-0.50	0.50
+5.000000000000000000e-01	5.000000000000000000e-01
+5.000000000000000000e-01	5.000000000000000000e-01
+5.000000000000000000e-01	5.000000000000000000e-01
+5.000000000000000000e-01	5.000000000000000000e-01
+5.000000000000000000e-01	5.000000000000000000e-01

tests/functional_tests/test_alt_allele_prob/true-alt_allele_prob-est_alt_allele_prob_multiple.txt

@@ -1,6 +1,6 @@
 MF_1	MF_2
-0.01	0.99
-0.01	0.99
-0.01	0.99
-0.01	0.99
-0.01	0.99
+9.999999776482582092e-03	9.900000095367431641e-01
+9.999999776482582092e-03	9.900000095367431641e-01
+9.999999776482582092e-03	9.900000095367431641e-01
+9.999999776482582092e-03	9.900000095367431641e-01
+9.999999776482582092e-03	9.900000095367431641e-01

tests/functional_tests/test_alt_allele_prob/true-alt_allele_prob-est_alt_allele_prob_multiple_individual.txt

@@ -1,6 +1,6 @@
 MF_1	MF_2
-0.01	0.99
-0.01	0.99
-0.50	0.50
-0.01	0.99
-0.01	0.99
+9.999999776482582092e-03	9.900000095367431641e-01
+9.999999776482582092e-03	9.900000095367431641e-01
+5.000083446502685547e-01	4.999749958515167236e-01
+9.999999776482582092e-03	9.900000095367431641e-01
+9.999999776482582092e-03	9.900000095367431641e-01

tests/functional_tests/test_alt_allele_prob/true-alt_allele_prob-est_alt_allele_prob_single.txt

@@ -1,6 +1,6 @@
 MF_1
-0.01
-0.01
-0.01
-0.01
-0.01
+9.999999776482582092e-03
+9.999999776482582092e-03
+9.999999776482582092e-03
+9.999999776482582092e-03
+9.999999776482582092e-03