diff create_config_file.py @ 0:f65530d07350 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit 1f1c277219ca756c9baa453592b455597fd593d8-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_config_file.py	Tue May 17 04:35:44 2016 -0400
@@ -0,0 +1,21 @@
+import argparse
+
+
+description = ("This script will create a configuration file for samples to be run in Breakdancer."
+               "If pooled analysis desired, only one config file needed for all samples."
+               "Otherwise, individual analysis requires individual config files for each sample.")
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--input_file", nargs="*", help="One or more alignment files")
+parser.add_argument("--mean", nargs="+", help="Mean insert size")
+parser.add_argument("--std_dev", nargs="+", help="The standard deviation of insert size")
+parser.add_argument("--read_length", nargs="+", help="Average read length")
+parser.add_argument("--sample_name", nargs="+", help="Sample name")
+parser.add_argument("--output_config_file", help="Name of the output config file")
+args = parser.parse_args()
+
+template = "map:{input_file}\tmean:{mean}\tstd:{std_dev}\treadlen:{read_length}\tsample:{sample_name}\texe:samtools view\n"
+with open(args.output_config_file, "w") as output:
+    for input_file, mean, std_dev, read_length, sample_name in zip(args.input_file, args.mean, args.std_dev, args.read_length, args.sample_name):
+        config_line = template.format(input_file=input_file, mean=mean, std_dev=std_dev, read_length=read_length, sample_name=sample_name)
+        output.write(config_line)
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