Add minimal logging to vtools

vtools/cli.py

@@ -7,6 +7,7 @@ vtools.cli
 :license: MIT
 """
 import json
+import logging
 import click
 from cyvcf2 import VCF, Writer
 
@@ -15,6 +16,13 @@ from .filter import FilterParams, FilterClass, Filterer
 from .stats import Stats
 from .gcoverage import RefRecord, region_coverages
 
+# Create logger and console handler
+logger = logging.getLogger('vtools')
+formatter = logging.Formatter('%(name)s - %(message)s')
+ch = logging.StreamHandler()
+ch.setFormatter(formatter)
+logger.addHandler(ch)
+
 
 @click.command()
 @click.option("-c", "--call-vcf", type=click.Path(exists=True),
@@ -36,8 +44,18 @@ from .gcoverage import RefRecord, region_coverages
 @click.option("-dc", "--discordant", type=click.Path(writable=True),
               help="Path to output discordant VCF file",
               required=False)
+@click.option("--log", type=click.Choice(['debug', 'info', 'warning', 'error',
+                                          'critical']), default='info')
 def evaluate_cli(call_vcf, positive_vcf, call_samples, positive_samples, stats,
-                 discordant):
+                 discordant, log):
+    # Set the level for the logger and the handler
+    logger.setLevel(log.upper())
+    ch.setLevel(log.upper())
+    logger.debug('Ontbuggen')
+    logger.info('informatie')
+    logger.warning('waarschuwing')
+    logger.error('fout')
+    logger.critical('kritiek')
     c_vcf = VCF(call_vcf, gts012=True)
     p_vcf = VCF(positive_vcf, gts012=True)
     st, disc = site_concordancy(c_vcf, p_vcf, call_samples,

vtools/evaluate.py

@@ -7,6 +7,7 @@ vtools.evaluate
 :license: MIT
 """
 from typing import List, Dict
+import logging
 
 from cyvcf2 import VCF
 
@@ -42,6 +43,14 @@ def site_concordancy(call_vcf: VCF,
                                    "het_concordant": 0, "sites_considered": 0,
                                    "total_sites": 0}
     """
+
+    logger = logging.getLogger('vtools.evaluate')
+
+    logger.debug('Ontbuggen')
+    logger.info('informatie')
+    logger.warning('waarschuwing')
+    logger.error('fout')
+    logger.critical('kritiek')
     if len(positive_samples) != len(call_samples):
         raise ValueError("Lists of samples must have same size")
 
@@ -70,6 +79,7 @@ def site_concordancy(call_vcf: VCF,
             pos_record.end
         )
 
+
         it = call_vcf(query_str)
         same = []
         for it_record in it:
@@ -79,6 +89,9 @@ def site_concordancy(call_vcf: VCF,
                     and it_record.ALT == pos_record.ALT):
 
                 same.append(it_record)
+                logger.debug('{} is excluded'.format(query_str))
+            else:
+                logger.debug('{} is included'.format(query_str))
 
         if len(same) != 1:
             continue