Replace format and % strings with f-strings

* wqflask/wqflask/marker_regression/gemma_mapping.py: Use f-strings
which are easier to read.
(generate_random_n_string): New function.

1 files changed, 69 insertions, 65 deletions

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 7a3d0312..83ebcdf9 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -20,6 +20,11 @@ if WEBSERVER_MODE == 'PROD':
     GEMMAOPTS = "-no-check"
 
 
+def generate_random_n_string(n):
+    return ''.join(random.choice(string.ascii_uppercase + string.digits)
+                   for _ in range(n))
+
+
 def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco,
               maf=0.01, first_run=True, output_files=None):
     """Generates p-values for each marker using GEMMA"""
@@ -29,89 +34,87 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco,
         genofile_name = this_dataset.group.name
 
     if first_run:
-        trait_filename = str(this_dataset.group.name) + "_" + str(this_trait.name) + "_" + \
-            ''.join(random.choice(string.ascii_uppercase + string.digits)
-                    for _ in range(6))
+        trait_filename = (f"{str(this_dataset.group.name)}_"
+                          f"{str(this_trait.name)}_"
+                          f"{generate_random_n_string(6)}")
         gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename)
 
-        if not os.path.isfile("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name)):
-            open("{}{}_output.assoc.txt".format(
-                webqtlConfig.GENERATED_IMAGE_DIR, genofile_name), "w+")
+        if not os.path.isfile(f"{webqtlConfig.GENERATED_IMAGE_DIR}"
+                              f"{genofile_name}_output.assoc.txt"):
+            open((f"{webqtlConfig.GENERATED_IMAGE_DIR}"
+                  f"{genofile_name}_output.assoc.txt"),
+                 "w+")
 
-        k_output_filename = this_dataset.group.name + "_K_" + \
-            ''.join(random.choice(string.ascii_uppercase + string.digits)
-                    for _ in range(6))
-        gwa_output_filename = this_dataset.group.name + "_GWA_" + \
-            ''.join(random.choice(string.ascii_uppercase + string.digits)
-                    for _ in range(6))
+        k_output_filename = (f"{this_dataset.group.name}_K_"
+                             f"{generate_random_n_string(6)}")
+        gwa_output_filename = (f"{this_dataset.group.name}_GWA_"
+                               f"{generate_random_n_string(6)}")
 
         this_chromosomes = this_dataset.species.chromosomes.chromosomes
-        this_chromosomes_name = [
-            this_chromosomes[chromosome].name for chromosome in this_chromosomes]
+        this_chromosomes_name = [this_chromosomes[chromosome].name
+                                 for chromosome in this_chromosomes]
 
         chr_list_string = ",".join(this_chromosomes_name)
         if covariates != "":
             gen_covariates_file(this_dataset, covariates, samples)
         if use_loco == "True":
-            generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json --loco ' + chr_list_string + ' -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
-                                                                                                                                                                                                    genofile_name,
-                                                                                                                                                                                                    TEMPDIR,
-                                                                                                                                                                                                    trait_filename,
-                                                                                                                                                                                                    flat_files(
-                                                                                                                                                                                                        'genotype/bimbam'),
-                                                                                                                                                                                                    genofile_name,
-                                                                                                                                                                                                    TEMPDIR,
-                                                                                                                                                                                                    k_output_filename)
-
+            generate_k_command = (f"{GEMMA_WRAPPER_COMMAND} --json --loco "
+                                  f"{chr_list_string} -- {GEMMAOPTS} "
+                                  f"-g {flat_files('genotype/bimbam')}/"
+                                  f"{genofile_name}_geno.txt -p "
+                                  f"{TEMPDIR}/gn2/{trait_filename}.txt -a "
+                                  f"{flat_files('genotype/bimbam')}/"
+                                  f"{genofile_name}_snps.txt -gk > "
+                                  f"{TEMPDIR}/gn2/{k_output_filename}.json")
             os.system(generate_k_command)
 
-            gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
-                                                                                                                                                                                      genofile_name,
-                                                                                                                                                                                      TEMPDIR,
-                                                                                                                                                                                      trait_filename)
+            gemma_command = (f"{GEMMA_WRAPPER_COMMAND} --json --loco "
+                             f"--input {TEMPDIR}/gn2/{k_output_filename}.json "
+                             f"-- {GEMMAOPTS} "
+                             f"-g {flat_files('genotype/bimbam')}/"
+                             f"{genofile_name}_geno.txt "
+                             f"-p {TEMPDIR}/gn2/{trait_filename}.txt ")
             if covariates != "":
-                gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 9 -maf %s > %s/gn2/%s.json' % (flat_files('mapping'),
-                                                                                                                 this_dataset.group.name,
-                                                                                                                 flat_files(
-                                                                                                                     'genotype/bimbam'),
-                                                                                                                 genofile_name,
-                                                                                                                 maf,
-                                                                                                                 TEMPDIR,
-                                                                                                                 gwa_output_filename)
+                gemma_command += (f"-c {flat_files('mapping')}/"
+                                  f"{this_dataset.group.name}_covariates.txt "
+                                  f"-a {flat_files('genotype/bimbam')}/"
+                                  f"{genofile_name}_snps.txt "
+                                  f"-lmm 9 -maf {maf} > {TEMPDIR}/gn2/"
+                                  f"{gwa_output_filename}.json")
             else:
-                gemma_command += ' -a %s/%s_snps.txt -lmm 9 -maf %s > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
-                                                                                         genofile_name,
-                                                                                         maf,
-                                                                                         TEMPDIR,
-                                                                                         gwa_output_filename)
+                gemma_command += (f"-a {flat_files('genotype/bimbam')}/"
+                                  f"{genofile_name}_snps.txt -lmm 9 -maf "
+                                  f"{maf} > "
+                                  f"{TEMPDIR}/gn2/{gwa_output_filename}.json")
 
         else:
-            generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
-                                                                                                                                                                     genofile_name,
-                                                                                                                                                                     TEMPDIR,
-                                                                                                                                                                     trait_filename,
-                                                                                                                                                                     flat_files(
-                                                                                                                                                                         'genotype/bimbam'),
-                                                                                                                                                                     genofile_name,
-                                                                                                                                                                     TEMPDIR,
-                                                                                                                                                                     k_output_filename)
+            generate_k_command = (f"{GEMMA_WRAPPER_COMMAND} --json -- "
+                                  f"{GEMMAOPTS} "
+                                  f" -g {flat_files('genotype/bimbam')}/"
+                                  f"{genofile_name}_geno.txt -p "
+                                  f"{TEMPDIR}/gn2/{trait_filename}.txt -a "
+                                  f"{flat_files('genotype/bimbam')}/"
+                                  f"{genofile_name}_snps.txt -gk > "
+                                  f"{TEMPDIR}/gn2/{k_output_filename}.json")
 
             os.system(generate_k_command)
 
-            gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 9 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
-                                                                                                                                                                                                        genofile_name,
-                                                                                                                                                                                                        flat_files(
-                                                                                                                                                                                                            'genotype/bimbam'),
-                                                                                                                                                                                                        genofile_name,
-                                                                                                                                                                                                        TEMPDIR,
-                                                                                                                                                                                                        trait_filename)
+            gemma_command = (f"{GEMMA_WRAPPER_COMMAND} --json --input "
+                             f"{TEMPDIR}/gn2/{k_output_filename}.json -- "
+                             f"{GEMMAOPTS} "
+                             f"-a {flat_files('genotype/bimbam')}/"
+                             f"{genofile_name}_snps.txt "
+                             f"-lmm 9 -g {flat_files('genotype/bimbam')}/"
+                             f"{genofile_name}_geno.txt -p "
+                             f"{TEMPDIR}/gn2/{trait_filename}.txt ")
 
             if covariates != "":
-                gemma_command += ' -c %s/%s_covariates.txt > %s/gn2/%s.json' % (
-                    flat_files('mapping'), this_dataset.group.name, TEMPDIR, gwa_output_filename)
+                gemma_command += (f" -c {flat_files('mapping')}/"
+                                  f"{this_dataset.group.name}"
+                                  f"_covariates.txt > "
+                                  f"{TEMPDIR}/gn2/{gwa_output_filename}.json")
             else:
-                gemma_command += ' > %s/gn2/%s.json' % (
-                    TEMPDIR, gwa_output_filename)
+                gemma_command += f" > {TEMPDIR}/gn2/{gwa_output_filename}.json"
 
         os.system(gemma_command)
     else:
@@ -129,8 +132,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco,
 def gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename):
     """Generates phenotype file for GEMMA"""
 
-    current_file_data = []
-    with open("{}/gn2/{}.txt".format(TEMPDIR, trait_filename), "w") as outfile:
+    with open(f"{TEMPDIR}/gn2/{trait_filename}.txt", "w") as outfile:
         for value in vals:
             if value == "x":
                 outfile.write("NA\n")
@@ -160,7 +162,9 @@ def gen_covariates_file(this_dataset, covariates, samples):
                     this_covariate_data.append("-9")
         covariate_data_object.append(this_covariate_data)
 
-    with open("{}/{}_covariates.txt".format(flat_files('mapping'), this_dataset.group.name), "w") as outfile:
+    with open((f"{flat_files('mapping')}/"
+               f"{this_dataset.group.name}_covariates.txt"),
+              "w") as outfile:
         for i in range(len(covariate_data_object[0])):
             for this_covariate in covariate_data_object:
                 outfile.write(str(this_covariate[i]) + "\t")
@@ -170,7 +174,7 @@ def gen_covariates_file(this_dataset, covariates, samples):
 def parse_loco_output(this_dataset, gwa_output_filename, loco="True"):
 
     output_filelist = []
-    with open("{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json") as data_file:
+    with open(f"{TEMPDIR}/gn2/{gwa_output_filename}.json") as data_file:
         data = json.load(data_file)
 
     files = data['files']