changeset 3:12c0699dcf22 draft

Uploaded updated useless line in script

--- a/Bt_detect_galaxy.py	Tue Mar 26 09:52:19 2024 +0000
+++ b/Bt_detect_galaxy.py	Tue Mar 26 11:29:21 2024 +0000
@@ -1,4 +1,3 @@
-#!/global/conda/envs/artwork/bin/python
 # -*- coding: iso-8859-1 -*-
 import os, sys
 import argparse
@@ -12,26 +11,24 @@
 	parser = argparse.ArgumentParser(description='Bacillus Thuringiensis serovars aizaiwai and kurstaki detection')
 						
 	parser.add_argument('-b', action="store", dest='blastx_output',
-						type=str, required=True, help='blastx output tabular file')		
+						type=str, required=True, help='blastx output tabular file')
 
 	parser.add_argument('-o', action="store", dest='output',
-						type=str, default="output.tsv", help='output file (default:output.tsv')	
+						type=str, default="output.tsv", help='output file (default:output.tsv')
 
 	parser.add_argument('-t', action="store", dest='decision_table',
 						type=str, default="table_bt.txt", help='Decision table (default:table_bt.txt)')
 						
 	parser.add_argument('-min_id', action="store", dest='min_identity',
-						type=str, default='90', help='minimum percent of blast identity (default:90)')					
+						type=str, default='90', help='minimum percent of blast identity (default:90)')
 
 	parser.add_argument('-min_cov', action="store", dest='min_coverage',
-						type=str, default="90", help='minimum percent of blast coverage (default:90)')	
+						type=str, default="90", help='minimum percent of blast coverage (default:90)')
 
 	return parser
 
 
-		
-		
-def decision_table_parser(file) :	
+def decision_table_parser(file) :
 
 	f = open(file, 'r')
 	lines = f.readlines()
@@ -64,8 +61,8 @@
 			i+=1
 			
 	return 	dico_marker, header_list, dico_association,result_key	
-		
-		
+
+
 def seqLen(fasta):
 
 	file = open(fasta,'r')
@@ -81,8 +78,8 @@
 			dico_sequence[id] = len
 	
 	return dico_sequence
-	
-	
+
+
 def blast_parser(blast_file, mincov, minid, dico_len):
 
 	file = open(blast_file,'r')
@@ -102,8 +99,8 @@
 			marker_list.append(line[1])
 	
 	return marker_list
-	
-	
+
+
 def assign(marker_found,dico_marker,header_list,dico_association,genome_id,result_key):
 	
 	group_list = []
@@ -136,26 +133,25 @@
 					break
 	
 	return result
-	
-	
-#main function	
-def main():	
+
 
-	
+#main function
+def main():
+
 	# Get arguments 
 	parser=get_parser()
-	
+
 	# Print parser.help if no arguments
 	if len(sys.argv)==1:
 		parser.print_help()
 		sys.exit(1)
-	
-	Arguments=parser.parse_args()	
-	
+
+	Arguments=parser.parse_args()
+
 	# Process decision table
 	dico_marker, header_list, dico_association,result_key = decision_table_parser(Arguments.decision_table)
 	dico_len = seqLen(Arguments.blastx_output)
-	
+
 	output_file = open(Arguments.output,'w')
 	genome_id = "sample"
 	blast_out = Arguments.blastx_output
@@ -163,8 +159,7 @@
 	result = assign(marker_list,dico_marker,header_list,dico_association,genome_id,result_key)
 	output_file.write(result+'\n')
 	output_file.close()	
-		
-		
+
+
 if __name__ == "__main__":
-	main()	   	
-	
+	main()
\ No newline at end of file