SUPER-FOCUS: A Python repository from rajaldebnath

#SUPER-FOCUS A tool for agile functional analysis of shotgun metagenomic data || version 0.27

(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

DOWNLOAD DATABASE

Program: superfocus__downloadDB.py: Downloads and formats the SUPER_FOCUS database for the available aligners (1) Usage

python superfocus__downloadDB.py aligner

#Example: python superfocus__downloadDB.py rapsearch blast diamond

You may choose as many aligners as you want among the three, as long as they are installed.

(2) Recommendations

- RAPSearch2 and DIAMOND don't work properly using a already formatted database with a newer version of the 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.

(1) SUPER-FOCUS USAGE

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

(2) Output

SUPER-FOCUS output will be add the folder selected in -dir

(3) Plotting output

Please read https://github.com/metageni/SUPER-FOCUS/tree/master/plotting_output for plotting your output

(4) Recommendations

- 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

(5) Dependencies

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 AND LICENSE

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/.

rajaldebnath/SUPER-FOCUS