Python Workflow.load Examples

Example #1

File: addexp_workflow_template.py Project: MrKriss/popGen

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 
#===============================================================================

subgroups = { 'zebra'  : '.*zebra.*',

Example #2

File: gz_clust_add_workflow_script.py Project: MrKriss/popGen

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}

subgroups = { 'zebra'  : '.*zebra.*',
            'gazelle' : '.*gazelle.*'}