Commit 8db81907 authored by peguerin's avatar peguerin
Browse files

stampa

parent eb3d0c37

README.md

+13 −1
Original line number Diff line number Diff line
@@ -31,6 +31,10 @@ You will also need to have the following programs installed on your computer. 


- [OBItools](https://pythonhosted.org/OBITools/welcome.html#installing-the-obitools)

- [ecoPCR](https://git.metabarcoding.org/obitools/ecopcr/wikis/home)

- [python 3.6.6](https://www.python.org/downloads/release/python-366/)

- `python 3 library` [biopython](https://biopython.org/)

- `python 3 library` [etetoolkit](http://etetoolkit.org/)





## Preparation
@@ -41,7 +45,7 @@ You will also need to have the following programs installed on your computer. 
## Build a reference database



* Overview of the steps

	1. Download the sequences

	1. Download the sequences

	2. Download the taxonomy

	3. Use [ecoPCR](https://git.metabarcoding.org/obitools/ecopcr/wikis/home)

 to simulate an *in silico* PCR
@@ -73,3 +77,11 @@ You can use the absolute path of the folder of your reference database as the `/ 
* [nextflow_obitools](https://gitlab.mbb.univ-montp2.fr/edna/nextflow_obitools)

* [snakemake_only_obitools](http://gitlab.mbb.univ-montp2.fr/edna/snakemake_only_obitools)



## Reference database in STAMPA format



Once you generated you're reference database, you need the `db_{prefix}.fasta` file (see [results](Results) section).

To convert your reference database in STAMPA format type :

```

python3 scripts/formatDB_obifasta_to_stampa.py -f db_{prefix}.fasta -o /path/to/reference_database_stampa.fasta

```

It will generate a file `/path/to/reference_database_stampa.fasta` which you can use as a reference database into the pipeline [bash_swarm](https://gitlab.mbb.univ-montp2.fr/edna/bash_swarm)
 
 No newline at end of file

scripts/formatDB_obifasta_to_stampa.py

0 → 100644
+72 −0
Original line number Diff line number Diff line 
#===============================================================================

#INFORMATIONS

#===============================================================================

"""

CEFE - EPHE - YERSIN 2018

guerin pierre-edouard

from reference database obitools fasta files, 

it creates a stampa-format reference database

"""

#===============================================================================

#USAGES

#===============================================================================

"""

input :

path to FASTA obitools file with "species=" information field available

output :

path to write the STAMPA-format FASTA reference databasae file

command : 

python3 ncbi_to_stampa.py -f input -o output

"""

#===============================================================================

#MODULES

#===============================================================================

import Bio

from Bio import SeqIO

from Bio.Alphabet import IUPAC

from Bio.Seq import Seq

from Bio.SeqRecord import SeqRecord

import argparse

from ete3 import NCBITaxa

#===============================================================================

#ARGUMENTS

#===============================================================================



parser = argparse.ArgumentParser(description='convert fasta obitools to stampa format')

parser.add_argument("-o","--output", type=str)

parser.add_argument("-f","--fasta",type=str)

#===============================================================================

#MAIN

#===============================================================================

args = parser.parse_args()

outputFile = args.output

fastaFile = args.fasta

ncbi = NCBITaxa()

mes_records=[]

for seq_record in SeqIO.parse(fastaFile, "fasta",alphabet=IUPAC.unambiguous_dna):

    local_id=seq_record.id

    sr_description=seq_record.description.split(';')

    #print(local_id)

    #print(sr_description)

    for elem in sr_description:

        #print(elem.split('=')[0])

        if len(elem) == 0:

            continue

        if elem.split('=')[0] == " species":

            cmd_get_dico="id_species="+str(elem.split('=')[1])

            exec(cmd_get_dico)

            if id_species != -1:

                lineage=ncbi.get_lineage(id_species)

                names = ncbi.get_taxid_translator(lineage)

                all_tax_species=""

                for taxid in lineage[2:]:

                    all_tax_species+=names[taxid]

                    all_tax_species+="|"

                all_tax_species=all_tax_species.replace(" ","+")

            else:

                continue

    local_seq=Seq(str(repr(str(seq_record.seq.lower()))).replace("'",""),IUPAC.unambiguous_dna)

    local_record=SeqRecord(local_seq,id=seq_record.id,description=all_tax_species[:-1])

    mes_records.append(local_record)

SeqIO.write(mes_records, outputFile, "fasta")