from classes.ChewbaccaCommand import ChewbaccaCommand
from Clean_Deep_Program_Macse import Clean_Deep_Program_Macse
[docs]class Clean_Deep_Command(ChewbaccaCommand):
"""Performs an intensive deep-cleaning of sequences to eliminate frameshifts, detect chimeras,
and determine sequence orientation. Input files to this command should first be dereplicated. Doing so will
reduce the total number of alignments required, and reduce computation time.
**Inputs**:
* One or more fasta/fastq files to deep clean (nucleotide sequences).
* One reference fasta (nucleotide sequences).
**Outputs**:
* \*_AA - Amino Acid Alignment file, including reference sequences.
* \*_log.csv - A log listing each input sequence, and deep cleaning results for each sequence.
* \*_NT - Nucleotide Alignment file, including reference sequences.
**Notes**:
* Sequences that do not meet quality cleaning standards are dropped.
* The output files contain reference sequences, and odd alignment characters. Both of these need to be \
removed by running the Clean_Deep_Repair Command.
**Example**:
::
Data.fasta
BIOCODE.fa
``$ python chewbacca.py macseAlign -i Data.fasta -o rslt -d BIOCODE.fa``
::
rslt/Data_AA
rslt/Data_NT
rslt/Data_log.csv
"""
supported_programs = [Clean_Deep_Program_Macse]
default_program = Clean_Deep_Program_Macse
command_name = "Clean_Deep"