'''
from utils.workflow import Workflow
'''----------------------------------------------------------------------------
Workflow script for Gazelles-Zebras RAD-data
-----------------------------------------------------------------------------'''
testing = False
experiment_name = '10percent-test'
description = 'A larger test set to test out the data on'
# Preprocessing
#===============================================================================
W = Workflow()
W.create_new(name='zebras-gazelles-test', testing=testing)
# Make sure barcodes and datafiles are in their right folders
if testing:
W.add_datafiles(data_files='testset_500.fastq.bgzf' , barcode_files='*[8].txt')
else:
W.add_datafiles(data_files='lane6*bgzf' , barcode_files='*[6].txt')
W.add_datafiles(data_files='lane8*bgzf' , barcode_files='*[8].txt')
# Set parameters
p = {'filtering' : {'propN': 0.1,
'phred': 25,
'cutsite_edit_dist' : 2,
from utils.workflow import Workflow
"""----------------------------------------------------------------------------
Workflow script for Gazelles-Zebras RAD-data
-----------------------------------------------------------------------------"""
experiment_name = ""
description = ""
dataset_name = ""
testing = False
# Preprocessing
# ===============================================================================
W = Workflow()
W.create_new(name=dataset_name, testing=testing)
# Make sure barcodes and datafiles are in their right folders
if testing:
W.add_datafiles(data_files="testset_500.fastq.bgzf", barcode_files="*[8].txt")
else:
W.add_datafiles(data_files="*.bgzf", barcode_files="*.txt")
W.add_datafiles(data_files="*.bgzf", barcode_files="*.txt")
# Set parameters
p = {
"filtering": {"propN": 0.1, "phred": 25, "cutsite_edit_dist": 2, "overhang_edit_dist": 0},
"cleaning": {"max_edit_dist": 1},
'''
from utils.workflow import Workflow
'''----------------------------------------------------------------------------
Workflow script Template for adding experiment to Gazelles-Zebras RAD-data
-----------------------------------------------------------------------------'''
experiment_name = ''
description = ''
dataset_name = ''
# Load previously processed data info
#===============================================================================
W = Workflow()
W.load(name=dataset_name)
# Clustering
#===============================================================================
W.add_experiment_name(experiment_name, description)
default_params = { 'c_thresh' : 0.90,
'n_filter' : 8,
'maskN' : False}
#===============================================================================
# Choose method to split files
#===============================================================================
'''
from utils.workflow import Workflow
'''----------------------------------------------------------------------------
Workflow script for Gazelles-Zebras RAD-data
-----------------------------------------------------------------------------'''
testing = False
experiment_name = 'gz_MIDs_95g1'
description = 'Cluster all MID tags separately at 95% identity all v all.'
# Load previously processed data info
#===============================================================================
W = Workflow()
W.load(name='gazelles-zebras')
# W.create_new(name='gazelles-zebras', testing=testing)
# Clustering
#===============================================================================
if testing:
W.add_experiment_name('gz-subgroups-test', 'Test for splitting files by subgroups')
else:
W.add_experiment_name(experiment_name, description)
default_params = { 'c_thresh' : 0.90,
'n_filter' : 8,
'maskN' : False}
