Update README.md

README.md

@@ -10,18 +10,15 @@ https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Do
 - genometools (v 1.5.8) with gt sketch -
 https://github.com/genometools/genometools
 
-#### Python3 libraries
-Program is running only on Python 3 version and uses non-standard libraries:
+#### Install
 
-- BioPython -
-http://biopython.org/
-- BCBio GFF -
-https://github.com/chapmanb/bcbb/tree/master/gff
-- networkx -
-https://networkx.github.io/
+```
+chmod +x setup.sh
+sudo ./setup.sh
+```
 
 #### Setting up the config
-Before usage, **python/config.py** needs to be set up:
+Before usage, **config.yml** needs to be set up:
 
 - ltr paths - executable, prosite and tRNAdb
 - ltr arguments 
@@ -30,12 +27,34 @@ Before usage, **python/config.py** needs to be set up:
 - blastx protein database (our database available at ... )
 - blastx arguments
 
+**Note**: `config.yml` is located by default in directory `/etc/nested/.`
+
+#### Usage
 ```
-Usage: python3 main.py [OPTIONS]
+Usage: nested-nester [OPTIONS] INPUT_FASTA
 
 Options:
-  -i, --input_fasta TEXT  Input fasta file.  [required]
   -s, --sketch_only       If true, nesting is not computed. Genes are sketched
                           only from existing gff files.
+  -d, --data_folder TEXT  Output data folder.
   --help                  Show this message and exit.
 ```
+
+```
+Usage: nested-generator [OPTIONS] INPUT_DB OUTPUT_DB
+
+Options:
+  -l, --baselength INTEGER        Baselength for generated elements.
+  -i, --number_of_iterations INTEGER
+                                  Number of iterations in generating.
+  -n, --number_of_elements INTEGER
+                                  Number of generated elements.
+  -f, --filter                    Filter database and create new one with
+                                  given output db path.
+  -s, --filter_string TEXT        Filter entries by given string [ONLY
+                                  RELEVANT WITH -filter OPTION].
+  -o, --filter_offset INTEGER     LTR offset allowed [ONLY RELEVANT WITH
+                                  -filter OPTION].
+  -d, --data_folder TEXT          Output data folder.
+  --help                          Show this message and exit.
+```