adding check_matrix_format.py to convert input expression matrices to…

… R-compatible format for read.table

Former-commit-id: 6087cbb

scripts/check_matrix_format.py

@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+
+"""
+Coverts a square expression matrix to an R-format compatible expression matrix
+"""
+
+
+# Import statements
+import argparse
+import csv
+import os
+
+__author__ = 'Jon Bistline'
+__copyright__ = 'Copyright 2018'
+__credits__ = ["Jon Bistline"]
+__license__ = 'BSD-3'
+__maintainer__ = 'Jon Bistline'
+__email__ = '[email protected]'
+__status__ = 'Development'
+
+def convert_matrix_format(input_matrix, delimiter, output_name):
+ """ Convert input expression matrix to R-compatible expression matrix (header line is 1 cell shorter than data lines)
+
+ :param input_matrix: Path to input expression matrix
+ :type input_matrix: String
+ :param delimiter: delimiter to parse input matrix with (tab, comma, etc.)
+ :type delimiter: String
+
+ """
+
+ if not input_matrix or not os.path.exists(input_matrix):
+ print("".join(["check_matrix_format.py:: ",
+ "Could not find input matrix : " + input_matrix]))
+
+ # read first line
+ with open(input_matrix, "r") as exp_matrix:
+ print("".join(["Opening input matrix and checking header format: ", input_matrix]))
+ print("".join(["Using delimiter: ", delimiter]))
+ rewrite_file = False
+ matrix = csv.reader(exp_matrix, delimiter=delimiter)
+ header_list = next(matrix)
+ # check if first value in header_list needs to be removed
+ headers_to_remove = ['GENE', 'gene', '']
+ if header_list[0] in headers_to_remove:
+ print("Input matrix is being converted to R format.")
+ rewrite_file = True
+ header_list.pop(0)
+ with open(output_name, 'w+') as new_expression_matrix:
+ writer = csv.writer(new_expression_matrix, delimiter=delimiter)
+ writer.writerow(header_list)
+ for line in matrix:
+ writer.writerow(line)
+
+ if rewrite_file is True:
+ print("".join(["Conversion complete, new output file: ", output_name]))
+ else:
+ os.rename(input_matrix, output_name)
+ print("".join(["No conversion necessary, input matrix is in R format already, renamed to new output file: ", output_name]))
+
+if __name__ == "__main__":
+
+ # Parse arguments
+ prsr_arguments = argparse.ArgumentParser(prog='check_matrix_format.py',
+ description='Coverts a square expression matrix to an R-compatible expression matrix.',
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+ # Add positional argument
+ prsr_arguments.add_argument("--input_matrix",
+ metavar="input_matrix",
+ help="Path to the input expression matrix")
+ prsr_arguments.add_argument("--delimiter",
+ metavar="delimiter",
+ default="\t",
+ help="delimiter to parse input matrix with (tab, comma, etc.)")
+ prsr_arguments.add_argument("--output_name",
+ metavar="output_name",
+ default="expression.r_format.txt",
+ help="path to output expression matrix")
+ args = prsr_arguments.parse_args()
+
+ # Run Script
+ convert_matrix_format(args.input_matrix, args.delimiter, args.output_name)