# Custom Metabarcoding Reference Database

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Scripts to convert FASTA files into reference database linked to NCBI taxonomy.

## Introduction

scripts to create our own reference database with our own sequences only and using the NCBI taxonomy



## Workflow

* 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

* 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`

3. verifier et corriger à la main le tableau `curated_taxon csv`

4. `raw fasta` `curated_taxon csv` --> validate --> `valide fasta` et mise à jour de la taxonomy


## Environment

To create environments with required softwares: 

```
conda env create -f envs/obitools_envs.yaml
conda env create -f envs/pylib_cbdr.yaml
```

* Obitools

```
conda activate obitools
```

* Required python libraries to build custom reference database

```
conda activate pylib_cbdr
```






## Usage

First time loading the taxdump

```
mkbdr validate --fasta resources/test/raw.fasta \
--ncbi_taxdump "TAXO/taxdump_2021.tar.gz" \
--output_prefix "test_raw"
```

taxdump previously loaded (faster)

```
mkbdr validate --fasta resources/test/raw.fasta \
--output_prefix "test_raw"
```

Apply curation

```
mkbdr validate --fasta resources/test/raw.fasta \
--curate curated_taxon.csv
--output_prefix "test_curated"
```

Generate a curation csv file

```
mkbdr curegen --fasta test_raw_faulty_taxon.fasta \
--output_prefix "test"
```

Specify the globalnames database to query

```
mkbdr curegen --fasta test_raw_faulty_taxon.fasta \
--output_prefix "test" \
--database_globalnames 'Catalogue of Life'
```



_______________________________________________________________________________


crash test
```
python3 mkbdr validate --fasta teleo_ok.fasta --curate curated_taxon.csv --output_prefix "truc"
```