--- a/screen_abricate_report.py	Thu Dec 19 20:31:11 2019 -0500
+++ b/screen_abricate_report.py	Thu Jan 02 17:14:34 2020 -0500
@@ -7,6 +7,27 @@
 import re
 
 
+class Range(object):
+    """
+    Used to limit the min_coverage and min_identity args to range 0.0 - 100.0
+    """
+    def __init__(self, start, end):
+        self.start = start
+        self.end = end
+
+    def __eq__(self, other):
+        return self.start <= other <= self.end
+
+    def __contains__(self, item):
+        return self.__eq__(item)
+
+    def __iter__(self):
+        yield self
+
+    def __repr__(self):
+        return str(self.start) + " - " + str(self.end)
+
+
 def parse_screen_file(screen_file):
     screen = []
     with open(screen_file) as f:
@@ -24,6 +45,16 @@
     return fieldnames
 
 
+def detect_gene(abricate_report_row, regex, min_coverage, min_identity):
+    gene_of_interest = bool(re.search(regex, abricate_report_row['GENE']))
+    sufficient_coverage = float(abricate_report_row['%COVERAGE']) >= min_coverage
+    sufficient_identity = float(abricate_report_row['%IDENTITY']) >= min_identity
+    if gene_of_interest and sufficient_coverage and sufficient_identity:
+        return True
+    else:
+        return False
+
+
 def main(args):
     screen = parse_screen_file(args.screening_file)
     gene_detection_status_fieldnames = ['gene_name', 'detected']
@@ -44,20 +75,25 @@
                 'detected': False
             }
             for abricate_report_row in abricate_report_reader:
-                if re.search(gene['regex'], abricate_report_row['GENE']):
+                if detect_gene(abricate_report_row, gene['regex'], args.min_coverage, args.min_identity):
                     gene_detection_status['detected'] = True
                     screened_report_writer.writerow(abricate_report_row)
             gene_detection_status_writer.writerow(gene_detection_status)
             f1.seek(0)  # return file pointer to start of abricate report
+            next(abricate_report_reader)
 
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser()
     parser.add_argument("abricate_report", help="Input: Abricate report to screen (tsv)")
     parser.add_argument("--screening_file", help="Input: List of genes to screen for (tsv)")
-    parser.add_argument("--screened_report", help=("Output: Screened abricate report ",
-                                                   "including only genes of interest (tsv)"))
-    parser.add_argument("--gene_detection_status", help=("Output: detection status for all genes ",
-                                                         "listed in the screening file (tsv)"))
+    parser.add_argument("--screened_report",
+                        help=("Output: Screened abricate report, including only genes of interest (tsv)"))
+    parser.add_argument("--gene_detection_status",
+                        help=("Output: detection status for all genes listed in the screening file (tsv)"))
+    parser.add_argument("--min_coverage", type=float,  default=90.0,
+                        choices=Range(0.0, 100.0), help=("Minimum percent coverage"))
+    parser.add_argument("--min_identity", type=float, default=90.0,
+                        choices=Range(0.0, 100.0), help=("Minimum percent identity"))
     args = parser.parse_args()
     main(args)