chore: added requirements, added output to function and misc stuff, added output to parser

requirements.txt

+csv
+glob
+io
+os
+matplotlib.pyplot
+

src/meanvariancefunction.py

@@ -6,15 +6,18 @@ import os
 import matplotlib.pyplot as plt
 
 
-def mean_variance(filepath: str) -> str:
+def mean_variance(filepath: str, output_dir: str = os.getcwd()+'/') -> str:
     """Given the counts observed for a given gene across all cells,
     calculate the mean and variance.
 
+    ! At the moment the function does not check the import files format,
+    be careful, and only add text files in the format geneid number_of_transcipts !
+
     Args:
-        directory with files of gene expression counts in individual cells.
+        directory with text files of gene expression counts in individual cells.
     Returns:
-        1. Path to Csv-formatted table with GeneID, Mean, Variance of the count.
-        2. Scatterplot of mean vs variance for all genes.
+        1. Path to Csv-formatted table with GeneID, Mean, Variance of the count, and
+        Scatterplot of mean vs variance for all genes.
 
     Raises:
         ValueError: If there are no files in directory
@@ -58,13 +61,14 @@ def mean_variance(filepath: str) -> str:
     plt.xlabel('mean')
     plt.ylabel('variance')
     plt.title('Mean gene expression vs. variance')
+    plt.savefig(output_dir+'/meanvarianceplot.png')
     plt.show()
     # Constructs csv file and saves it in the users directory
-    path = os.path.expanduser("~")+'/results_mean_var_function.csv'
+    path = output_dir+'/results_mean_var_function.csv'
     with open(path, 'w') as csv_file:
         filewriter = csv.writer(csv_file, delimiter=',', quotechar='|',
                                 quoting=csv.QUOTE_MINIMAL)
         filewriter.writerow(['geneid', 'mean', 'variance'])
         for id in gene_counts.keys():
             filewriter.writerow([id, mean[id], variance[id]])
-    return path
+    return output_dir

src/parser_meanvar.py

+import argparse
+from meanvariancefunction import mean_variance as mv
+
+parser = argparse.ArgumentParser(
+        description=('Calculates mean and variance for all gene entries' +
+                     'and plots mean against variance'),
+        add_help=False,
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+parser.add_argument('-i', '--input', required=True, type=str,
+                    help='input file path')
+parser.add_argument('-o', '--output', required=True, type=str,
+                    help='output file path')
+parser.add_argument("-h", "--help", action="help",
+                    help="show this help message and exit")
+
+args = parser.parse_args()
+input_path = args.input
+output_path = args.output
+
+meanvarf = mv(input_path, output_path)