from classes.ChewbaccaCommand import ChewbaccaCommand
from otu.Query_OTU_DB_Program_Vsearch import Query_OTU_DB_Program_Vsearch
[docs]class Query_OTU_DB_Command(ChewbaccaCommand):
"""Aligns sequences in a fasta file against those in a reference database in order to determine OTU identity.
Only alignment based identification using vsearch is currenty available
**Inputs**:
* One or more fasta files containing sequences to identify.
* A curated fasta file of high quality sequences and known species.
* A database containing taxonomic identifiers for sequences in the curated fasta file.
**Outputs**:
* A :ref:`.tax`.
**Notes**:
* The files COI.fasta and ncbi.db are included in the Chewbacca Docker distributions.
**Example**:
::
~/ARMS/refs/
COI.fasta # A precompiled fasta file of COI data from NCBI.
>94483305
AGGACGGATCAGACGAAGAGGGGCGTTTGGTATTGGGTTATGGCAGGGGGTTTTATATTGATAATTGTTGTGATGAAATT
GATGGCCCCTAAGATAGAGGAGACACCTGCTAGGTGTAAGGAGAAGATGGTTAGGTCTACGGAGGCTCCAGGGTGGGAGT
ncbi.db # A precompiled database of (Taxa) for the entries in 'COI.fasta'.
data/
Data.fasta:
>seq1
GAATAGGTGTTGGTATAGAATGGGGTCTCCTCCTCCGGCGGGGTCGAAGAAGGTGGTGTTGAGGTTGCGGTCTGTTAGTAGTATAGTGATGCCAGCAG
CTAGGACTGGGAGAGATAGGAGAAGTAGGACTGCTGTGATTAGGACGGATCAGACGAAGAGGGGCGTTTGGTATTGGGTTATGGCAGGGGGTTTTATA
TTGATAATTGTTGTGAGGAAATTGATGGCCCCTAAGATAGAGGAGACACCTGCTAGGTGTAAGGAGAAGATGGTTAGGTCTACGGAGGCTCCAGGGTG
GGAGTAGTTCCCTGCTAA
``$ python chewbacca.py query_db -i Data.fasta -o out/ -r ~/ARMS/refs/COI.fasta -d ~/ARMS/refs/ncbi.db``
::
rslt/
Data_result.out
seq1 94483305 99.4 173 55.4 Chordata:Mammalia:Primates:Hominidae:Homo:Homo sapiens
"""
supported_programs = [Query_OTU_DB_Program_Vsearch]
default_program = Query_OTU_DB_Program_Vsearch
command_name = "Query OTU Identity"