Adding logging calls

andrew/pipeline.log

@@ -0,0 +1,9 @@
+2017-07-20 16:23:37,154 - logArgs - INFO: Arguments for Test:
+2017-07-20 16:23:37,155 - logArgs - INFO: Arguments uniform_bins: 10
+2017-07-20 16:23:37,155 - logArgs - INFO: Arguments vcfname: example/locus8.vcf.gz
+2017-07-20 16:23:37,155 - logArgs - INFO: Arguments random_seed: 83441029
+2017-07-20 16:23:37,155 - logArgs - INFO: Arguments statistic_file: example/locus8.windowed.weir.fst
+2017-07-20 16:23:37,155 - logArgs - INFO: Arguments calc_statistic: windowed-weir-fst
+2017-07-20 16:23:37,155 - logArgs - INFO: Arguments sampling_scheme: random
+2017-07-20 16:23:37,155 - logArgs - INFO: Arguments sample_size: 200
+2017-07-20 16:23:37,155 - logArgs - INFO: Arguments statistic_window_size: 10000

andrew/tester.py

@@ -0,0 +1,73 @@
+import os, sys, csv, argparse, logging, random, pysam
+import numpy as np
+import pandas as pd
+from collections import defaultdict
+
+# Load path from Jared's directory, remove when not needed
+sys.path.insert(0, os.path.abspath(os.path.join(os.pardir, 'jared')))
+
+from parse_functions import defaultsDictForFunction, getConfigFilename, makeRequiredList, getArgsWithConfig
+from logging_module import initLogger
+
+def sampler_parser():
+    '''Sampler Argument Parser - Assigns arguments from command line.'''
+
+    def parser_confirm_file ():
+        '''Custom action to confirm file exists'''
+        class customAction(argparse.Action):
+            def __call__(self, parser, args, value, option_string=None):
+                if not os.path.isfile(value):
+                    raise IOError # File not found
+                setattr(args, self.dest, value)
+        return customAction
+
+    sampler_parser = argparse.ArgumentParser()
+
+    # Input arguments
+    sampler_parser.add_argument("vcfname", metavar='VCF_Input', help = "Input VCF filename", type = str, action = parser_confirm_file())
+    sampler_parser.add_argument('--statistic-file', help='Specifies the statistic file for filtering', required = True, type = str, action = parser_confirm_file())
+
+    # Statistic based arguments.
+    statistic_list = ['windowed-weir-fst', 'TajimaD']
+    statistic_default = 'windowed-weir-fst'
+    sampler_parser.add_argument('--calc-statistic', metavar = '{' + ', '.join(statistic_list) + '}', help = 'Specifies the statistic calculated ', type=str, choices = statistic_list, default = statistic_default)
+
+    sampler_parser.add_argument('--statistic-window-size', help = 'Specifies the size of window calculations', type = int, default = 10000)
+
+    # Sampling methods. Currently mutually exclusive to only allow a single sampling method
+    sampling_list = ['uniform', 'random']
+    sampling_default = 'random'
+    sampler_parser.add_argument('--sampling-scheme', metavar = '{' + ', '.join(sampling_list) + '}', help = 'Specifies the sampling scheme ', type=str, choices = sampling_list, default = sampling_default)
+
+    # Sampling options
+    sampler_parser.add_argument('--uniform-bins', help="Number of bins in uniform sampling", type = int, default = 10)
+    sampler_parser.add_argument('--sample-size', help="Total sample size. If using the uniform sampling scheme, this number must be divisible by the bins", type = int, default = 200)
+
+    # Other options
+    sampler_parser.add_argument('--random-seed', help="Defines the random seed value for the random number generator", type = int, default = random.randint(1, 1000000000))
+
+    return sampler_parser.parse_args()
+
+def logArgs(args, pipeline_function):
+    logging.info('Arguments for %s:' % pipeline_function)
+    for k in vars(args):
+        logging.info('Arguments %s: %s' % (k, vars(args)[k]))
+
+def run ():
+
+    # Get arguments from command line
+    sampler_args = sampler_parser()
+
+    #required_args = ['vcfname','statistic_file','genename']
+    #args = getArgsWithConfig(parser,sys_args,required_args,'vcf_ref_to_seq')
+
+    # Set the random seed
+    random.seed(sampler_args.random_seed)
+
+    logArgs(sampler_args, 'Test')
+
+    print sampler_args
+
+if __name__ == "__main__":
+    initLogger()
+    run()

andrew/vcf_calc.py

@@ -9,7 +9,7 @@
 # Insert Jared's directory path, required for calling Jared's functions. Change when directory structure changes.
 sys.path.insert(0, os.path.abspath(os.path.join(os.pardir, 'jared')))
 
-#from logging_module import initLogger
+from logging_module import initLogger
 
 def vcf_calc_parser(passed_arguments):
     '''VCF Argument Parser - Assigns arguments from command line'''
@@ -66,6 +66,12 @@ def __call__(self, parser, args, value, option_string=None):
     else:
         return vcf_parser.parse_args()
 
+def logArgs(args, pipeline_function):
+    ''' Logs arguments from argparse system. Likely should be'''
+    logging.info('Arguments for %s:' % pipeline_function)
+    for k in vars(args):
+        logging.info('Arguments %s: %s' % (k, vars(args)[k]))
+
 def run (passed_arguments = []):
     '''
     Statistic calculation using VCFTools.