From 3e463f1b86528f388f5c8becff988df6ef696ef4 Mon Sep 17 00:00:00 2001
From: bistline <bistline@broadinstitute.org>
Date: Thu, 29 Mar 2018 15:38:49 -0400
Subject: [PATCH] adding check_matrix_format.py to convert input expression
 matrices to R-compatible format for read.table

Former-commit-id: 6087cbb8985bbc3dc1c1fc41f359f272b7e7f28e
---
 scripts/check_matrix_format.py | 82 ++++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)
 create mode 100644 scripts/check_matrix_format.py

diff --git a/scripts/check_matrix_format.py b/scripts/check_matrix_format.py
new file mode 100644
index 00000000..6fd561aa
--- /dev/null
+++ b/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__ = 'bistline@broadinstitute.org'
+__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)