added script to merge matrices and updated docs

docs/helper.md

@@ -105,4 +105,17 @@ required data is included here as well. Note that this script requires sklearn a
     python3 pca_powerlaw.py ./data/sbi.expression.matrix.tpm.txt ./data/sbi_annotation.txt ./data/sbi.power_law.R07.txt
 
 
-
+## Utilities
+
+### merge_matrix.py
+
+In case samples for one (!) species were processed in two or more batches, this script can be used to merge the 
+expression matrices.
+
+*Note that to obtain co-expression networks using the merged matrix LSTrAP needs to be run, using the merged expression 
+matrix, skipping all steps before the construction of co-expression.*
+
+*Only merge raw matrices with raw, tpm with tpm and rpkm with rpkm!*
+
+
+    python3 merge_matrix.py matrix_one.txt matrix_two.txt matrix_merged.txt  

helper/merge_matrix.py

@@ -0,0 +1,43 @@
+import argparse
+import sys
+
+import pandas as pd
+
+
+def merge_matrix(first, second, output):
+    """
+    This function will take two matrices and merge them
+
+    :param first:   first input matrix (path)
+    :param second:  second input matrix (path)
+    :param output:  output matrix (path)
+    """
+
+    df_first = pd.read_table(first, header=0, index_col=0)
+    df_second = pd.read_table(second, header=0, index_col=0)
+
+    if df_first.shape[0] != df_second.shape[0]:
+        print("WARNING: attempting to merge two matrices with a different number of rows", file=sys.stderr)
+
+    df_output = pd.concat([df_first, df_second], axis=1)
+
+    if any([df_first.shape[0] != df_output.shape[0],
+           df_second.shape[0] != df_output.shape[0],
+           df_output.shape[1] != df_first.shape[1] + df_second.shape[1]]):
+        print("WARNING: output matrix has an unexpected shaped", file=sys.stderr)
+
+    df_output.index.name = 'gene'
+    df_output.to_csv(output, sep='\t')
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser(prog="./merge_matrix.py")
+
+    parser.add_argument('first',  help='first LSTrAP matrix to merge')
+    parser.add_argument('second', help='second LSTrAP matrix to merge')
+    parser.add_argument('output', help='path to output')
+
+    args = parser.parse_args()
+
+    merge_matrix(args.first, args.second, args.output)