diff format_reago_input_files.py @ 0:13dd84cab09e draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit f5be73e67192909db96dfab214f4360eb41757a4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/format_reago_input_files.py	Sat Apr 27 17:59:57 2024 +0000
@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import argparse
+
+
+def add_read_pair_num(input_filepath, output_filepath, read_pair_num):
+    to_add = "." + str(read_pair_num)
+    with open(input_filepath, "r") as input_file:
+        with open(output_filepath, "w") as output_file:
+            for line in input_file:
+                if line.startswith(">"):
+                    split_line = line.split()
+                    seq_id = split_line[0]
+                    if seq_id.rfind(to_add) != (len(seq_id) - len(to_add)):
+                        split_line[0] = seq_id + to_add
+                    output_file.write(" ".join(split_line) + "\n")
+                else:
+                    output_file.write(line)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--r1_input", required=True)
+    parser.add_argument("--r2_input", required=True)
+    parser.add_argument("--r1_output", required=True)
+    parser.add_argument("--r2_output", required=True)
+    args = parser.parse_args()
+
+    add_read_pair_num(args.r1_input, args.r1_output, 1)
+    add_read_pair_num(args.r2_input, args.r2_output, 2)