chip-create-run 902 Bytes
Newer Older
1
2
3
4
5
6
7
8
#!/usr/bin/env python
from chipathlon.db import MongoDB
import chipathlon.conf
import argparse
import yaml
import pprint

parser = argparse.ArgumentParser(description="Create a run file from a list of experiment accessions.")
9
10
11
parser.add_argument("-H", "--host", dest="host", default="localhost", help="Database host. (default: %(default)s)")
parser.add_argument("-u", "--username", dest="username", help="Database username (if required).")
parser.add_argument("-p", "--password", dest="password", help="Database password (if required).")
12
13
parser.add_argument("-n", "--name", dest="name", required=True, help="Name of the run file to create.")
parser.add_argument("-f", "--file_type", dest="file_type", default="fastq", help="Type of files to extract (fastq or bam).")
14

15
parser.add_argument("-a", "--accessions", dest="accessions", nargs="+", required=True, help="List of experiment accessions to load.")