MyNCList is an implementation of the NCList data structure within a MySQL database. The included python script reads data stored in a .BED file, organizes it into the NCList structure and uploads the data to MySQL, where stored procedures allow for in-place insertions and deletions, along with efficient interval-based querying.
MyNCList requires Python2.7, MySQL-python, and a MySQL database in
which to store the NCList structure. Installation should automatically
install MySQL-python and can install MySQL locally if specified.
If setuptools is not installed, you may download it from pypi:
https://pypi.python.org/pypi/setuptools
It is recommended that users install from the contents of dist/.
Automated Linux install:
cd dist/
sudo MyNCList-install.sh
or
cd dist/
sudo MyNCList-install.sh --mysql
If access to MySQL is not available, the second option will install mysql
onto your local linux machine, and create a database called nclist to be
used by MyNCList. Users should update their configuration files to reflect
this information.
Users with access to MySQL should create this database manually and specify the information in the configuration file. MyNCList.py will not attempt to create, delete, or modify any database besides those specified in configuration files.
For manual Linux installation:
cd dist/
tar -zxvf MyNCList-1.0.tar.gz
cd MyNCList-1.0
sudo python setup.py install
For manual Windows installation:
cd dist/
-Unzip MyNCList-1.0.zip-
cd MyNCList-1.0
python setup.py install
Configuration options for MyNCList should be specified in a config file, with
a space separating the configuration parameter and its value. A sample config
file is included with the distributable. MySQL tables will be created following
the convention DBNAME.LABEL_TABLENAME (e.g. nclist.sample_masterkey).
MyNCList will overwrite existing tables if necessary, so unique labels are
strongly encouraged.
Database Parameters:
DBHOST MySQL hostname
DBUSER MySQL user
DBPASS MySQL password
DBNAME MySQL database
Required Parameters:
BEDFILE Location of source .BED file
OFFSET Location chromosome base position offsets file
WORKDIR Working directory for intermediate files
LABEL Label for this set of annotations
Optional Parameters:
MEMBERSHIP Nest interval within the [first,last] valid parent
REPORTS Output additional intermediate files? [yes,no]
CONCAT_DUPS Concatenate annotations for duplicate intervals? [yes,no]