readme update

README.md

@@ -4,11 +4,11 @@
 
 
 
-Scripts to convert FASTA files into reference database linked to NCBI taxonomy.
+Scripts to convert FASTA files into reference database with NCBI taxonomy.
 
 ## Introduction
 
-scripts to create our own reference database with our own sequences only and using the NCBI taxonomy
+**mkbdr** is a python program designed to create reference database from FASTA file using the NCBI taxonomy. It also provides tools to assist and perform taxonomy curation on the input FASTA file.
 
 
 
@@ -17,28 +17,29 @@ scripts to create our own reference database with our own sequences only and usi
 * inputs:
     * FASTA file
 
-0. get raw fasta files of new sequences with species-names
-1. Extract sequence name
-2. Check sequence name format
-3. Check sequences format (iuapc ambiguity, gaps)
-4. Correct NCBI-taxonomy species name (this is semi-automatic)
-5. Attribute NCBI-taxonomy taxid
-6. Extract names with missing taxid
-    1. Attribute NCBI-taxonomy taxid of genus
-    2. Run obitaxonommy command for unattributed taxid species
-7. Write fasta file of sequences with their taxid and complete genus-species name
+
+1. Check FASTA format
+2. Check species name format
+3. Check DNA sequence format
+4. Check species name against NCBI taxonomy
+5. Attribute NCBI taxid
+6. Write `valid`, `faulty_taxon` and `faulty_format` FASTA files
+7. Curate species name using `curation` CSV file
+8. Write new nodes in NCBI taxonomy for unattributed taxid species
+9. Write `valid` FASTA files
 
 * outputs:
     * formatted FASTA file
     * .ldx new nodes for missing taxid into the taxonomy to link to existing genus/family taxid
 
-1. `raw fasta` --> validate --> `valide fasta` `faulty_format fasta` `faulty_taxon fasta`
 
-2. `faulty_taxon fasta` --> curate (actuellement Laetitia qui fait ce job) --> `curated_taxon csv`
+1. `raw fasta` --> validate --> `valid fasta` `faulty_format fasta` `faulty_taxon fasta`
+
+2. `faulty_taxon fasta` --> curegen --> `curation csv`
 
-3. verifier et corriger à la main le tableau `curated_taxon csv`
+3. verifier et corriger à la main le tableau `curation csv`
 
-4. `raw fasta` `curated_taxon csv` --> validate --> `valide fasta` et mise à jour de la taxonomy
+4. `raw fasta` `curation csv` --> validate --> `valid fasta` et mise à jour de la taxonomy
 
 
 ## Environment