Python modules and command line tools for accessing database of NGSV.
- Python (v2.7)
- pysam (>= v0.7)
- MySQL-python
- Cython
- MySQL
$ python setup.py install
ngsv uses MySQL database. First, create database.
$ ngsv initdb [--dbuser DBUSER] [--dbpassword DBPASSWORD]
$ ngsv loadsam [--dbuser DBUSER] [--dbpassword DBPASSWORD] samfile1 samfile2 ...
$ ngsv loadbed [--dbuser DBUSER] [--dbpassword DBPASSWORD] bedfile1 bedfile2 ...
$ ngsv loadcytoband [--dbuser DBUSER] [--dbpassword DBPASSWORD]
$ ngsv loadrefgene [--dbuser DBUSER] [--dbpassword DBPASSWORD]
You can see more detail usage by -h option.
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.