from classes.ChewbaccaCommand import ChewbaccaCommand
from Query_OTU_Fasta_Program_Vsearch import Query_OTU_Fasta_Program_Vsearch
[docs]class Query_OTU_Fasta_Command(ChewbaccaCommand):
"""Aligns sequences in a fasta file against those in a reference fasta in order to determine OTU identity.
**Inputs**:
* One or more fasta files containing sequences to identify.
* A curated fasta file of high quality sequences and known species.
* A two-column, tab-delimited text file mapping sequence names in the curated fasta file to taxonomic \
identifiers.
**Outputs**:
* A :ref:`.tax`.
**Notes**:
* The files 'bold.fna' and 'seq_lin.mapping' are included in the Chewbacca Docker distributions.
**Example**:
::
~/ARMS/data/
bold.fna # A precompiled fasta file of data from BOLD.
>GBMAA1117-14
GGGCTTTTGCGGGTATGATAGGAACAGCATTTAGTATGCTTATTAGGTTAGAACTATCTTCCCCAGGGTCTATGTTAGGAGATGATCATTTATATAAT
GTTATAGTAACAGCTCATGCATTTGTAATGATATTTTTTTTAGTTATGCCAGTAATGATTGGGGGTTTTGGTAATTGGTTAGTACCTTTATATATTGG
TGCCCCGGATATGGCTTTTCCTAGATTAAATAATATTAGTTTTTGGTTATTACCTCCGGCGCTTACTTTATTATTAGGTTCGGCTTTTGTAGAACAAG
GGGCTGGGACAGGTTGGACAGTTTATCCGCCTTTATTTAGTATTCAAACTCATTCTGGGGGGTCTGTGGATATGGTAATATTTAGTTTACATTTAGCT
GGAATATCTTCTATATTAGGGGCTATGAATTTTATAACAACAATCTTTAATATGAGGTCTCCGGGAGTAACTATGGATAGAATGCCTTTATTTGTTTG
ATCTGTTTTAGTAACTGCTTTTTTATTATTATTATCATTGCCAGTATTAGCTGGTGCCATAACAAGTCTTTTAACCGATCGAGATTTTAATACTACAT
TT
seq_lin.mapping # A precompiled two-column tab file of (Taxa) for the entries in 'bold.fna'.
GBMAA1117-14 Animalia;Porifera;Demospongiae;Haplosclerida;Phloeodictyidae;;Calyx;Calyx podatypa
./
Data.fasta:
>seq1
ACTATCAGGCATTCAAGCCCATTCAGGGGGAGCAGTAGATATGGCTATATTTAGTCTACATCTAGCTGGTGTATCCTCTATTTTAAGTTCTATAAACT
TTATAACTACTATAATTAATATGAGGGTTCCTGGGATGAGTATGCATAGATTACCTCTATTCGTATGGTCTGTATTAGTTACTACAATATTATTGTTG
TTATCTTTACCAGTATTAGCTGGTGGAATTACAATGTTATTGACAGATAGAAATTTTAATACAACATTCTTTGACCCTGCGGGAGGAGGAGATCCTAT
TTTATTCCAGCACTTATTT
``$ python chewbacca.py query_fasta -i Data.fasta -o rslt -r ~/ARMS/data/bold.fna -x ~/ARMS/data/seq_lin.mapping``
::
rslt/
Data_result.out
seq1 GBMAA1117-14 90.6 265 84.7 Animalia;Porifera;Demospongiae;Haplosclerida;Phloeodictyidae;;Calyx;Calyx podatypa
"""
supported_programs = [Query_OTU_Fasta_Program_Vsearch]
default_program = Query_OTU_Fasta_Program_Vsearch
command_name = "Query OTU Identity"
def execute_command(self):
self.get_program(self.args.program).execute_program()