drep 4.0.2__py3-none-any.whl

drep/d_workflows.py

@@ -0,0 +1,135 @@
+#!/usr/bin/env python3
+
+import logging
+import os
+import pandas as pd
+import sys
+
+import drep.WorkDirectory
+import drep.d_cluster.controller
+import drep.d_filter
+import drep.d_cluster
+import drep.d_choose
+import drep.d_bonus
+import drep.d_evaluate
+
+def dereplicate_wrapper(wd,**kwargs):
+    validate_dereplicate(wd, **kwargs)
+
+    message = """\
+***************************************************
+    ..:: dRep dereplicate Step 1. Filter ::..
+***************************************************
+    """
+    logging.info(message)
+
+    # Pop these arguments they're not there for future operations
+    genomes = kwargs.pop('genomes',None)
+    Chdb = kwargs.pop('Chdb',None)
+    drep.d_filter.d_filter_wrapper(wd, genomes = genomes, Chdb = Chdb, **kwargs)
+
+    message = """\
+***************************************************
+    ..:: dRep dereplicate Step 2. Cluster ::..
+***************************************************
+    """
+    logging.info(message)
+    drep.d_cluster.controller.d_cluster_wrapper(wd, **kwargs)
+
+    message = """\
+***************************************************
+    ..:: dRep dereplicate Step 3. Choose ::..
+***************************************************
+    """
+    logging.info(message)
+    drep.d_choose.d_choose_wrapper(wd, **kwargs)
+
+    message = """\
+***************************************************
+    ..:: dRep dereplicate Step 4. Evaluate ::..
+***************************************************
+    """
+    logging.info(message)
+    if kwargs.get('gen_warnings', False):
+        evaluate='23'
+    else:
+        evaluate = '3'
+    drep.d_evaluate.d_evaluate_wrapper(wd, evaluate=evaluate, **kwargs)
+
+    message = """\
+***************************************************
+    ..:: dRep dereplicate Step 5. Analyze ::..
+***************************************************
+    """
+    logging.info(message)
+    if kwargs.get('skip_plots', False):
+        to_plot = []
+    else:
+        to_plot = 'a'
+    drep.d_analyze.d_analyze_wrapper(wd, plots=to_plot, **kwargs)
+
+    loc = drep.WorkDirectory.WorkDirectory(wd).location
+    message = """\
+
+$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
+
+    ..:: dRep dereplicate finished ::..
+
+Dereplicated genomes................. {0}
+Dereplicated genomes information..... {2}
+Figures.............................. {1}
+Warnings............................. {3}
+
+$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
+    """.format(loc + '/dereplicated_genomes/', loc + '/figures/', \
+                loc + '/data_tables/Widb.csv', loc + '/log/warnings.txt')
+    logging.info(message)
+
+def compare_wrapper(wd,**kwargs):
+    validate_compare(wd, **kwargs)
+
+    message = """\
+***************************************************
+    ..:: dRep compare Step 1. Cluster ::..
+***************************************************
+    """
+    logging.info(message)
+    drep.d_cluster.controller.d_cluster_wrapper(wd, **kwargs)
+
+    message = """\
+***************************************************
+    ..:: dRep compare Step 2. Evaluate ::..
+***************************************************
+    """
+    logging.info(message)
+    drep.d_evaluate.d_evaluate_wrapper(wd, evaluate = '2', **kwargs)
+
+    message = """\
+***************************************************
+    ..:: dRep compare Step 3. Analyze ::..
+***************************************************
+    """
+    logging.info(message)
+    drep.d_analyze.d_analyze_wrapper(wd, plots = '1234', **kwargs)
+
+    loc = drep.WorkDirectory.WorkDirectory(wd).location
+    message = """\
+
+$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
+
+    ..:: dRep compare finished ::..
+
+Genome comparison data............... {0}
+Figures.............................. {1}
+Warnings............................. {3}
+
+$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
+    """.format(loc + '/data_tables/', loc + '/figures/', \
+                loc + '/data_tables/Widb.csv', loc + '/log/warnings.txt')
+    logging.info(message)
+
+def validate_dereplicate(wd, **kwargs):
+    pass
+
+def validate_compare(wd, **kwargs):
+    pass