Updated to call East African H58 sublineages

Updated version now calls: 
- 4.3.1.1.EA1 (H58 lineage I, East Africa 1)
- 4.3.1.2.EA2 (H58 lineage II, East Africa 2)
- 4.3.1.2.EA3 (H58 lineage II, East Africa 3)

--version flag added to coincide with future releases

genotyphi.py

@@ -9,7 +9,7 @@
 # Dependencies:
 #	 SAMtools (v1.2) and bcftools (v1.2) are required to genotype from BAMs.
 #
-# Last modified - Sep 3rd, 2020
+# Last modified - December 6th, 2020
 #
 
 from argparse import (ArgumentParser, FileType)
@@ -20,11 +20,14 @@
 import datetime
 from subprocess import call, check_output, CalledProcessError, STDOUT
 
+__version__ = '1.7.0'
 
 def parse_args():
 	"Parse the input arguments, use '-h' for help"
 	parser = ArgumentParser(description='VCF to Typhi genotypes')
-	parser.add_argument('--mode', required=True,
+	parser.add_argument('--version', action='version', version='GenoTyphi v' + __version__,
+		help="Show GenoTyphi version number and exit")
+	parser.add_argument('--mode', required=False,
 		help='Mode to run in based on input files (vcf, bam, or vcf_parsnp)')
 	parser.add_argument(
 		'--vcf', nargs='+', type=str, required=False,
@@ -55,28 +58,21 @@ def parse_args():
 		2723724, 3437570, 1780319, 1535365, 1792810, 3062270, 1799842, 432732, 3069182, 2732615, 3770391, 2269835,
 		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]
+		3498544,2424394,2272144,561056,3164873,
+		751854,4680610,2587488]
 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', 'C', 'G', 'A','G','A','A','A','A',
+			   'A','T','A']
 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']
+		  '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']
 
 ### QRDR SNP definitions
 
@@ -189,7 +185,7 @@ def parseGeno(this_groups, proportions):
 		elif level == 1:
 			primary.append(group)
 
-	# fix 4.3.1/4.3.1.1/4.3.1.2/4.3.1.P1/4.3.1.3 nesting
+	# fix 4.3.1/4.3.1.1/4.3.1.2/4.3.1.P1/4.3.1.3/EA nesting
 	if ('4.3.1.3' in subclades) and ('4.3.1' in subclades):
 		subclades.remove('4.3.1')
 	if ('4.3.1.1' in subclades) and ('4.3.1' in subclades):
@@ -200,6 +196,18 @@ def parseGeno(this_groups, proportions):
                 subclades.remove('4.3.1')
         if('4.3.1.1.P1' in subclades) and ('4.3.1.1' in subclades):
                 subclades.remove('4.3.1.1')
+	if('4.3.1.1.EA1' in subclades) and ('4.3.1.1' in subclades):
+		subclades.remove('4.3.1.1')
+	if('4.3.1.1.EA1' in subclades) and ('4.3.1' in subclades):
+		subclades.remove('4.3.1')
+	if('4.3.1.2.EA2' in subclades) and ('4.3.1.2' in subclades):
+		subclades.remove('4.3.1.2')
+	if('4.3.1.2.EA2' in subclades) and ('4.3.1' in subclades):
+		subclades.remove('4.3.1')
+	if('4.3.1.2.EA3' in subclades) and ('4.3.1.2' in subclades):
+		subclades.remove('4.3.1.2')
+	if('4.3.1.2.EA3' in subclades) and ('4.3.1' in subclades):
+		subclades.remove('4.3.1')
 
 	# fix 3.3.2.Bd nesting
 	if ('3.3.2.Bd1' in subclades) and ('3.3.2' in subclades):