diff add_sample_name_as_first_line.py @ 0:231b21337c43 draft

planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/add_sample_name_as_first_line.py	Thu Sep 27 17:05:18 2018 -0400
@@ -0,0 +1,23 @@
+import sys
+import argparse
+import re
+
+def Parser():
+  the_parser = argparse.ArgumentParser(description="add sample name as first line of a tab file")
+  the_parser.add_argument('--input', required=True, action="store", type=str, help="input tab file")
+  the_parser.add_argument('--output', required=True,  action="store", type=str, help="output file")
+  the_parser.add_argument('--sample', required=True, action="store", type=str, help="sample name to add as the first line of input file")
+  args = the_parser.parse_args()
+  return args
+
+args=Parser()
+
+sample_name = re.sub('[_12]*.fastq.gz', '', args.sample.rstrip().lstrip())
+
+with open(args.input) as input:
+	with open(args.output, 'w') as output:
+		output.write(sample_name+"\n")
+		for line in input:
+			output.write(line)
+
+