Genotypes 2.1.7.1 and 2.1.7.2 added

genotyphi.py

@@ -9,7 +9,7 @@
 # Dependencies:
 #	 SAMtools (v1.2) and bcftools (v1.2) are required to genotype from BAMs.
 #
-# Last modified - December 6th, 2020
+# Last modified - March 20th, 2021
 #
 
 from argparse import (ArgumentParser, FileType)
@@ -20,7 +20,7 @@
 import datetime
 from subprocess import call, check_output, CalledProcessError, STDOUT
 
-__version__ = '1.7.1'
+__version__ = '1.8.0'
 
 def parse_args():
 	"Parse the input arguments, use '-h' for help"
@@ -59,20 +59,24 @@ def parse_args():
 		4215341, 4602946, 3368641, 2245432, 3164162, 3923165, 1811809, 3729635, 3817752, 183033, 1615350, 2342045,
 		3996717, 2640029, 989024, 3806278, 1611156, 2348902, 1193220, 3694947, 955875,
 		3498544,2424394,2272144,561056,3164873,
-		751854,4680610,2587488]
+		751854,4680610,2587488,
+		4286788,3967063]
+
 snp_alleles = ['T', 'A', 'C', 'A', 'A', 'T', 'A', 'C', 'T', 'A', 'T', 'T', 'A', 'T', 'T', 'G', 'G', 'A', 'A', 'A', 'T',
 			   'A', 'T', 'A', 'A', 'A', 'A', 'T', 'C', 'A', 'C', 'A', 'A', 'A', 'T', 'T', 'T', 'T', 'G', 'C', 'A', 'T',
 			   'T', 'C', 'C', 'T', 'G', 'A', 'T', 'G', 'C', 'T', 'T', 'A', 'A', 'A', 'T', 'T', 'T', 'T', 'T', 'A', 'T',
 			   'A', 'T', 'A', 'A', 'T', 'C', 'G', 'A','G','A','A','A','A',
-			   'A','T','A']
+			   'A','T','A',
+			   'T','T']
 groups = ['0.1', '0.0.1', '0.0.2', '0.0.3', '0.1.1', '0.1.2', '0.1.3', '1', '1.1', '1.1.1', '1.1.2', '1.1.3', '1.1.4',
 		  '1.2', '1.2.1', '2', '2.0.1', '2.0.2', '2.1', '2.1.1', '2.1.2', '2.1.3', '2.1.4', '2.1.5', '2.1.6', '2.1.7',
 		  '2.1.8', '2.1.9', '2.2', '2.2.1', '2.2.2', '2.2.3', '2.2.4', '2.3', '2.3.1', '2.3.2', '2.3.3', '2.3.4',
 		  '2.3.5', '2.4', '2.4.1', '2.5', '2.5.1', '3', '3.0.1', '3.0.2', '3.1', '3.1.1', '3.1.2', '3.2', '3.2.1',
 		  '3.2.2', '3.3', '3.3.1', '3.4', '3.5', '3.5.1', '3.5.2', '3.5.3', '3.5.4', '4', '4.1', '4.1.1', '4.2',
 		  '4.2.1', '4.2.2', '4.2.3', '4.3.1', '4.3.1.1', '4.3.1.2', '4.3.1.1.P1',
 		  '3.3.2','3.3.2.Bd1','3.3.2.Bd2','4.3.1.3','2.5.2',
-		  '4.3.1.1.EA1','4.3.1.2.EA2','4.3.1.2.EA3']
+		  '4.3.1.1.EA1','4.3.1.2.EA2','4.3.1.2.EA3',
+		  '2.1.7.1','2.1.7.2']
 
 ### QRDR SNP definitions
 
@@ -215,6 +219,12 @@ def parseGeno(this_groups, proportions):
 	if ('3.3.2.Bd2' in subclades) and ('3.3.2' in subclades):
 		subclades.remove('3.3.2')
 
+		# fix 2.1.7/2.1.7.1/2.1.7.2 nesting
+	if ('2.1.7.1' in subclades) and ('2.1.7' in subclades):
+		subclades.remove('2.1.7')
+	if ('2.1.7.2' in subclades) and ('2.1.7' in subclades):
+		subclades.remove('2.1.7')
+
 	# fix 2.3, 2.2 nesting
 	if ('2.2' in clades) and ('2.3' in clades):
 		clades.remove('2.2')