update readme

README.md

@@ -1,12 +1,15 @@
-# SUPER-FOCUS
-SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data
-(c) Silva, G. G. Z., Green K., B. E. Dutilh, and R. A. Edwards.
+![](logo/superfocus_logo_small.png "Logo")
 
-If you use SUPER-FOCUS in your research, please cite:
+### SUPER-FOCUS: A tool for agile functional analysis of metagenomic data
+* [Installation](#installation)
+* [Dependencies](#dependencies)
+* [Aligners](#aligners)
+* [Download SUPER-FOCUS Database](#database)
+* [Running SUPER-FOCUS](#run)
+* [General Recomendations](#recomendations)
+* [Ouput](#output)
+* [Citing](#citing)
 
-    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
 
 ## Installation
 This will give you command line program:
@@ -21,19 +24,19 @@ or
 	# install super-focus
 	cd SUPER-FOCUS && python setup.py install
 
-### Dependencies
+## Dependencies
 - [Python 3.6](http://www.python.org/download)
 - [Numpy 1.12.1](https://github.com/numpy/numpy)
 - [SciPy 0.19.0](https://github.com/scipy/scipy)
 
-### Sequence aligners
+## Aligners
 One of the below aligners:
 - [DIAMOND 0.9.14](http://ab.inf.uni-tuebingen.de/software/diamond)
 - [RAPSearch2 2.24](http://rapsearch2.sourceforge.net)
 - [BLAST 2.6.0](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
 
 
-### Download SUPER-FOCUS database
+## Database
 Use `superfocus_downloadDB` to download and format the SUPER-FOCUS database
 for the available aligners:
 
@@ -50,12 +53,12 @@ re-run `superfocus_downloadDB` in case any aligner was updated on your
 system.
 
 
-### Run SUPER-FOCUS
+### Run
 The main SUPER-FOCUS program is `superfocus`. Here is a list of the
 available command line options:
 
 	-h print help
-	
+
 	-q FASTA/FASTQ
 		Path to directory with FASTA/FASTQ file(s)
 
@@ -64,7 +67,7 @@ available command line options:
 
 	-o string
 		output prefix (default 'output_')
-	
+
 	-mi float
 		minimum identity (default 60 %)
 
@@ -81,7 +84,7 @@ available command line options:
 		e-value (default 0.00001)
 
 	-db string
-		database (DB_90, DB_95, DB_98, or DB_100; default DB_98)
+		database (DB_90, DB_95, DB_98, or DB_100; default DB_90)
 
 	-p int
 		amino acid input; 0 nucleotides; 1 amino acids (default 0)
@@ -90,37 +93,26 @@ available command line options:
 		aligner choice (rapsearch (only fasta files) or diamond; default rapsearch)
 
 	-fast int
-		runs RAPSearch2 or DIAMOND on fast mode - 0 (False) / 1 (True) (default: 1)	
-  
+		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)
 
-### Usage example
-```
-superfocus -q query.fasta -dir output_dir
-```
-This will run SUPER-FOCUS using `query.fasta` as a query, and output results into `myOutputDirectory`.
+	Usage example: superfocus -q query.fasta -dir output_dir
 
-#### General recommendations
+## Recomendations
 - The FOCUS reduction is not necessary if not wanted (it is off by default: set `-focus 1` to run FOCUS reduction)
 - Run RAPSearch for short sequences, it is less sensitive for long sequences
 - Primarily use DIAMOND for large datasets only. It is slower than blastx for small datasets
 - BLAST is known for being really slow
 
-### Output
+## Output
 SUPER-FOCUS output will be add the folder selected by the `-dir` argument.
 
-# Copyright and License
-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.
+## Citing
 
-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.
+If you use SUPER-FOCUS in your research, please cite:
 
-You should have received a copy of the GNU General Public License along with
-this program.  If not, see <http://www.gnu.org/licenses/>.
+    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

superfocus_app/superfocus.py

@@ -211,7 +211,7 @@ def parse_args():
     parser.add_argument("-t", "--threads",  help="Number Threads used in the k-mer counting (Default: 4)",
                         default="4")
     parser.add_argument("-e", "--evalue",  help="e-value (default 0.00001)", default="0.00001")
-    parser.add_argument("-db", "--database",  help="database (DB_90, DB_95, DB_98, or DB_100; default DB_98)",
+    parser.add_argument("-db", "--database",  help="database (DB_90, DB_95, DB_98, or DB_100; default DB_90)",
                         default="DB_90")
     parser.add_argument("-p", "--amino_acid",  help="amino acid input; 0 nucleotides; 1 amino acids (default 0)",
                         default="0")
@@ -222,7 +222,6 @@ def parse_args():
     parser.add_argument("-n", "--normalise_output",  help="normalises each query counts based on number of hits; "
                                                           "0 doesn't normalize; 1 normalizes (default: 1)", default="1")
     parser.add_argument("-m", "--focus",  help="runs FOCUS; 1 does run; 0 does not run: default 0", default="0")
-    parser.add_argument("-d", "--work_directory",  help="Work directory")
     parser.add_argument("-b", "--alternate_directory",  help="Alternate directory for your databases", default="")
 
     return parser.parse_args()