(c) Silva, G. G. Z., Green K., B. E. Dutilh, and R. A. Edwards: SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data. Bioinformatics. 2015 Oct 9. pii: btv584. website: https://edwards.sdsu.edu/SUPERFOCUS
Program: superfocus__downloadDB.py: Downloads and formats the SUPER_FOCUS database for the available aligners (1) Usage
python superfocus__downloadDB.py aligner
You may choose as many aligners as you want among the three, as long as they are installed.
- RAPSearch2 and DIAMOND don't work properly using a already formatted database with a newer version of the
aligner. Thus, please re-run 'superfocus__downloadDB.py' in the case of any aligner was updated in the
system.
Program: superfocus.py: SUPER-FOCUS main program Options:
-h print help
-q FASTA/FASTQ
query file (FASTA or FASTQ format) or folder with multiple FASTA/FASTQ files when -m 1
-dir string
output directory
-o string
project name (default 'my_project')
-mi float
minimum identity (default 60 %)
-ml int
minimum alignment (amino acids) (default: 15)
-focus int
runs FOCUS; 1 does run; 0 does not run: default 0
-t int
number of threads (default 8 )
-e float
e-value (default 0.00001)
-db string
database (DB_90, DB_95, DB_98, or DB_100; default DB_98)
-p int
amino acid input; 0 nucleotides; 1 amino acids (default 0)
-k int
keep original tabular output. 0 delete it / 1 keep it (default 0)
-a string
aligner choice (rapsearch, blast (only fasta files), diamond; default rapsearch)
-fast int
runs RAPSearch2 or DIAMOND on fast mode - 0 (False) / 1 (True) (default: 1)
-n int
normalizes each query counts based on number of hits; 0 doesn't normalize; 1 normalizes (default: 1)
-r string
use only the subsystems in the organisms predicted by "-focus"– ncbi / rast annotation (default: ncbi)
example> python superfocus.py -q query.fasta -dir myOutputdirectory
SUPER-FOCUS output will be add the folder selected in -dir
Please read https://github.com/metageni/SUPER-FOCUS/tree/master/plotting_output for plotting your output
- The FOCUS reduction is not necessary if not wanted (set -focus 0)
- Run RAPSearch for short sequences. it is less sensitive for long sequences
- How BLAST if you want the result to be the most sensitive as possible
- Only use DIAMOND for large datasets. It is slower than blastx for small datasets
- Python >= 2.6.X < 3.Y: http://www.python.org/download
- Jellyfish: http://www.cbcb.umd.edu/software/jellyfish
- Numpy: http://sourceforge.net/projects/numpy/files/NumPy
- SciPy: http://sourceforge.net/projects/scipy
One of the below aligners:
- RAPSearch2: http://rapsearch2.sourceforge.net
- DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond
- BLAST: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST
Copyright (C) 2014-2017 Genivaldo Gueiros Z. Silva
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.