modes and minor fix

bin/txM_lca

@@ -81,19 +81,28 @@ def p_pair(pl1, pl2, tax_d):
 		tag_l[1] = tag_d[tax_2]
 	tag = ''.join(tag_l)
 
-	if tax_1 == '-':
-		p_tax = tax_2
-	elif tax_1 == '0':
-		p_tax = tax_1
-		if tax_2 != '-' and tax_2 != '0':
+	if opt.d_mode == 'p':
+		if tax_1 == '-':
 			p_tax = tax_2
-	else:
-		p_tax = tax_1
-		if tax_2 != '-' and tax_2 != '0' and tax_2 != tax_1:
-			if tax_2 in tax_d[tax_1][3].split(':'):
-				pass
-			elif tax_1 in tax_d[tax_2][3].split(':'):
+		elif tax_1 == '0':
+			p_tax = tax_1
+			if tax_2 != '-' and tax_2 != '0':
 				p_tax = tax_2
+		else:
+			p_tax = tax_1
+			if tax_2 != '-' and tax_2 != '0' and tax_2 != tax_1:
+				if tax_2 in tax_d[tax_1][3].split(':'):
+					pass
+				elif tax_1 in tax_d[tax_2][3].split(':'):
+					p_tax = tax_2
+				else:
+					p_tax = lca(sorted([tax_d[tax_1][3], tax_d[tax_2][3]]))
+	elif opt.d_mode == 'P':
+		if tax_1 == '-' or tax_2 == '-':
+			p_tax = '-'
+		else:
+			if tax_1 == '0' or tax_2 == '0':
+				p_tax = '0'
 			else:
 				p_tax = lca(sorted([tax_d[tax_1][3], tax_d[tax_2][3]]))
 	tax_str = '\t'.join([tag] + tax_d[p_tax][:3])
@@ -128,12 +137,12 @@ parser.add_option(
 	)
 
 parser.add_option(
-	"-p",
-	metavar = "FLAG",
-	dest = "paired",
-	action = 'store_true',
-	default = False,
-	help = "Paired LCA determination (only for interleaved input; default = False)"
+	"-m",
+	metavar = "STR",
+	type = "string",
+	dest = "d_mode",
+	default = 's',
+	help = "Taxa determination mode ('s' single-end; 'p' paired-end; 'P' paired-end strict; default = 's')"
 	)
 
 parser.add_option(
@@ -188,11 +197,11 @@ if __name__ == '__main__':
 		map_file = open(opt.map_file, 'r')
 	else:
 		map_file = stdin
-	if not opt.paired:
+	if opt.d_mode == 's':
 		for l in map_file:
 			stdout.write(p_rec(l.strip(), tax_d, excluded) + '\n')
 			stderr.write(p_rec(l.strip(), tax_d, excluded) + '\n')
-	elif opt.paired:
+	elif opt.d_mode == 'p' or opt.d_mode == 'P':
 		while 1:
 			l1 = map_file.readline()
 			if not l1:

bin/txM_report

@@ -72,12 +72,12 @@ parser.add_option(
 	)
 
 parser.add_option(
-	"-m",
-	metavar = "STR",
-	type = "string",
-	dest = "d_mode",
-	default = 's',
-	help = "Taxa determination mode ('s' single-end; 'p' paired-end; 'P' paired-end strict; default = 's')"
+	"-p",
+	metavar = "FLAG",
+	dest = "paired",
+	action = 'store_true',
+	default = False,
+	help = "Paired LCA determination (only for interleaved input; default = False)"
 	)
 
 parser.add_option(
@@ -91,7 +91,7 @@ parser.add_option(
 
 (opt, args) = parser.parse_args()
 
-if opt.tax_file == None or opt.d_mode not in ['s', 'p', 'P'] or opt.out_prefix == None:
+if opt.tax_file == None or opt.out_prefix == None:
 	parser.print_help()
 	exit(-1)
 
@@ -135,12 +135,10 @@ if __name__ == '__main__':
 		la = l.strip().split('\t')
 		tax_id = la[0] 
 		path = tax_d[tax_id][3]
-		if opt.d_mode == 's':
-			counts = int(la[4])
-		elif opt.d_mode == 'p':
+		if opt.paired:
 			counts = int(la[7]) + int(la[8])
-		elif opt.d_mode == 'P':
-			counts = int(la[7])
+		else:
+			counts = int(la[4])
 		tax_d[tax_id][4] = counts
 		for node in path:
 			tax_d[node][5] += counts
@@ -158,7 +156,7 @@ if __name__ == '__main__':
 	for tax_id in tax_d:
 		tax_d[tax_id][6] -= tax_d[tax_id][4]
 		path = tax_d[tax_id][3]
-		if tax_d[tax_id][5] > min_c and len(path) > 1 :
+		if tax_d[tax_id][5] >= min_c and len(path) > 1 :
 			tax_d[path[-2]][6] -= tax_d[tax_id][5]
 
 

taxMaps

@@ -639,8 +639,7 @@ if __name__ == '__main__':
 	tax_command += ' 2> /dev/null \\\n\t| ' 
 	tax_command +=  'txM_lca '
 	tax_command += '-t ' + rp(tax_lnk, run_dir) + ' '
-	if det_mode == 'p' or det_mode == 'P':
-		tax_command += '-p '
+	tax_command += '-m ' + det_mode + ' '
 	tax_command += '2> ' + rp(map_dir + '/' + prefix + '.merged.map.lca', run_dir)
 	tax_command += ' \\\n\t| '
 	tax_command += 'txM_summary '
@@ -657,7 +656,8 @@ if __name__ == '__main__':
 	rep_command = 'cat ' + rp(out_dir + '/' + prefix + '.merged.map.lca.summary', out_dir) + ' \\\n\t| '
 	rep_command += 'txM_report '
 	rep_command += '-t ' + rp(tax_lnk, out_dir) + ' '
-	rep_command += '-m ' + det_mode + ' '
+	if det_mode == 'p' or det_mode == 'P':
+		rep_command += '-p '
 	rep_command += '-c ' + rep_cutoff + ' '
 	rep_command += '-o ' + prefix + ' '