from classes.ChewbaccaCommand import ChewbaccaCommand
from Preclean_Program_Bayeshammer import Preclean_Program_Bayeshammer
[docs]class Preclean_Command(ChewbaccaCommand):
""" Attempts to fix minor sequencing errors caused by pyrosequencing. By reducing errors prior to sequence assembly,
a greater number of paired reads can be sucessfully assembled. Matching forward and reverse files should be \
identically named,
except for a <forward>/<reverse> suffix that indicates the read orientation. The two suffix conventions below \
are supported. Choose ONE suffix style and stick to it! Mixed suffixes are not supported.
::
_forwards/_reverse
and
_R1/_R2
**Inputs**:
* fastq file(s) with left reads .
* fastq file(s) with right reads .
**Outputs**:
* <left reads file>_corrected.fastq file(s).
* <right reads file>_corrected.fastq file(s).
**Example**:
Assuming a forwards read file 'Data_R1.fq' and a reverse reads file 'Data_R1.fq',
::
./
Data_R1.fq
Data_R2.fq
``$ python chewbacca.py preclean -f Data_R1.fq -r Data_R2.fq -o rslt``
::
rslt/
Data_R1_corrected.fq
Data_R2_corrected.fq
"""
supported_programs = [Preclean_Program_Bayeshammer]
default_program = Preclean_Program_Bayeshammer
command_name = "Preclean"