diff --git a/README.md b/README.md index 3011e28..1472e8b 100644 --- a/README.md +++ b/README.md @@ -1 +1,20 @@ -**refGene-sort** \ No newline at end of file +**refGene-sort** + +Utility to sort refGene tab-delimited annotation files from Genome Browser (DB dumps) +```bash +usage: refgene-sort [-h] [-t TMP] [-q QUERRY] [-s ORDER] -i INPUT -o OUTPUT + +refGene annotation sorter + +optional arguments: + -h, --help show this help message and exit + -t TMP, --tmp TMP Temp folder to store sqlite db file + -q QUERRY, --querry QUERRY + Custom select querry. Table name should be refGene + -s ORDER, --order ORDER + Ordering option + -i INPUT, --input INPUT + Input file to location + -o OUTPUT, --output OUTPUT + Output file to location +``` \ No newline at end of file diff --git a/refgene_sort/main.py b/refgene_sort/main.py index f03ab47..13b779c 100644 --- a/refgene_sort/main.py +++ b/refgene_sort/main.py @@ -10,7 +10,7 @@ def arg_parser(): """Returns argument parser""" - parser = argparse.ArgumentParser(description='refGene annotation sorter parser') + parser = argparse.ArgumentParser(description='refGene annotation sorter') parser.add_argument ("-t", "--tmp", help="Temp folder to store sqlite db file", default=None) parser.add_argument ("-q", "--querry", help="Custom select querry. Table name should be refGene", default="SELECT * FROM refGene") parser.add_argument("-s", "--order", help="Ordering option", default='')