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Update README
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michael-kotliar committed Jul 31, 2017
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21 changes: 20 additions & 1 deletion README.md
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**refGene-sort**
**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
```
2 changes: 1 addition & 1 deletion refgene_sort/main.py
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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='')
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