pymegablast is a python wrapper for megablast, allowing multiple tasks
required by the PGx center.
pymegablast should work on MacOS, even though it hasn't been fully tested for
full compatibility.
Here are the requirements that must be installed before pymegablast:
$ pymegablast.py --help
usage: pymegablast.py [-h] [-v] -i FILE [-w] [-wl INT] [-d PATH] [-W INT]
[-s INT] [-o DIR]
Runs pymegablast (version 0.3).
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
Input Files:
-i FILE, --input FILE
The file containing the sequence(s).
Sequence(s) Pre-Processing:
-w, --window If set to True, the sequence(s) will be split by a
window of X characters (see -wl/--window-length
option). [Default: False]
-wl INT, --window-length INT
The window size (if -w/--window option is used).
[Default: 20]
MegaBlast Options:
-d PATH, --database PATH
The database to use for the search. [Default:
/mnt/isi/reference/Genome_Build_37/chromosomes]
-W INT, --word-size INT
The word size for MegaBlast. [Default: 10]
-s INT, --minimal-hit-score INT
The minimal hit score for MegaBlast. [Default: 17]
Output Files:
-o DIR, --output-dir DIR
The name of the output directory. [Default:
megablast.2015-01-23_11.36.35]