from classes.ChewbaccaCommand import ChewbaccaCommand
from otu.Build_OTU_Table_Program_Chewbacca import Build_OTU_Table_Program_Chewbacca
[docs]class Build_OTU_Table_Command(ChewbaccaCommand):
"""Builds an OTU table using a .groups, .samples, and .barcodes file. The OTU table shows OTU (group) abundance by
sample.
**Inputs**:
* One or more :ref:`.samples`.
* One or more :ref:`.barcodes`.
* one or more :ref:`.groups`.
**Outputs**:
* matrix.txt - A tab-delimited table mapping OTUs (groups) to their abundance in each sample.
**Notes**:
* A sequence name may not appear in more than one group file (or more than one line in a gropus file for \
that matter!).
**Example**:
::
./
test.barcodes
Sample1 aaaaaa
Sample2 aaaaat
Sample3 aaaaac
Sample4 aaaaag
test.groups
seq3 seq3 seq5 seq4
seq1 seq2 seq1 seq7 seq6
test.samples
seq1 Sample1
seq2 Sample1
seq3 Sample1
seq4 Sample2
seq5 Sample2
seq6 Sample2
seq7 Sample3
``$ python chewbacca.py build_matrix -b test.barcodes -g test.groups -s test.samples -o rslt/``
::
rslt/
matrix.txt
OTU Sample1 Sample2 Sample3 Sample4
seq3 1 2 0 0
seq1 2 1 1 0
"""
supported_programs = [Build_OTU_Table_Program_Chewbacca]
default_program = Build_OTU_Table_Program_Chewbacca
command_name = "Build OTU Table"