Adding shebang to python scripts and dos2unix on python scripts

guiguimartin · Jan 28, 2021 · ca557ea · ca557ea
1 parent 418ff43
commit ca557ea
Show file tree

Hide file tree

Showing 31 changed files with 3,102 additions and 3,079 deletions.
diff --git a/LICENSE b/LICENSE
diff --git a/bin/BLAT_gros.py b/bin/BLAT_gros.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+# -*- coding:Utf-8 -*-
 
 #
 #  Copyright 2014 CIRAD

diff --git a/bin/Filter_single_hit_sam.py b/bin/Filter_single_hit_sam.py
@@ -1,103 +1,105 @@
-
-#
-#  Copyright 2014 CIRAD
-#
-#  This program is free software; you can redistribute it and/or modify
-#  it under the terms of the GNU General Public License as published by
-#  the Free Software Foundation; either version 3 of the License, or
-#  (at your option) any later version.
-#
-#  This program is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#  GNU General Public License for more details.
-#
-#  You should have received a copy of the GNU General Public License
-#  along with this program; if not, see <http://www.gnu.org/licenses/> or
-#  write to the Free Software Foundation, Inc.,
-#  51 Franklin Street, Fifth Floor, Boston,
-#  MA 02110-1301, USA.
-#
-#
-
-
-import optparse, os, shutil, subprocess, sys, tempfile, fileinput, ConfigParser, operator, time
-
-
-def find_info(LINE):
-	dic = {}
-	for n in LINE[11:]:
-		liste = n.split(':')
-		if len(liste) > 2:
-			dic[liste[0]] = liste[2]
-	return dic
-
-def CIGAR(mot):
-	if 'N' in mot:
-		sys.exit('N in mot')
-	elif 'P' in mot:
-		sys.exit('P in mot')
-	elif '=' in mot:
-		sys.exit('= in mot')
-	elif 'X' in mot:
-		sys.exit('X in mot')
-	else:
-		mot_split = mot.replace('M',' M ').replace('D',' D ').replace('I',' I ').replace('S',' S ').replace('H',' H ').split()
-	total = 0
-	while mot_split:
-		if mot_split[1] == 'M' or mot_split[1] == 'D':
-			total = total + int(mot_split[0])
-		del mot_split[0]
-		del mot_split[0]
-	return total
-
-def sam2tab(LINE):
-	TOTAL = CIGAR(LINE[5])
-	if LINE[1] == '0':
-		return LINE[0]+'\t'+LINE[2]+'\t-\t1\t-\t'+LINE[3]+'\t'+str(int(LINE[3])+TOTAL)+'\t1'
-	elif LINE[1] == '16':
-		return LINE[0]+'\t'+LINE[2]+'\t-\t1\t-\t'+LINE[3]+'\t'+str(int(LINE[3])+TOTAL)+'\t-1'
-	else:
-		sys.exit('Probleme in sam flag '+LINE[1])
-
-def __main__():
-	#Parse Command Line
-	parser = optparse.OptionParser(usage="python %prog [options]\n\nProgram designed by Guillaume MARTIN : [email protected]")
-	# Wrapper options. 
-	parser.add_option( '', '--sam', dest='sam', help='The sam file')
-	parser.add_option( '', '--dif', dest='dif', help='The minimal difference between the best and second hit accepted to consider the hit as single')
-	parser.add_option( '', '--type', dest='type', help='The output type, sam or tab')
-	(options, args) = parser.parse_args()
-
-	min_dif = int(options.dif)
-
-	file = open(options.sam)
-	if options.type != 'sam' and options.type != 'tab':
-		sys.exit('Output option is not recognised')
-	for line in file:
-		data = line.split()
-		if data:
-			if data[0][0] != '@':
-				if data[1] != '256' and data[1] != '272':
-					dico = find_info(data)
-					if 'XS' in dico:
-						if abs(int(dico['AS'])-int(dico['XS'])) >= min_dif:
-							if options.type == 'sam':
-								print('\t'.join(data))
-							else:
-								if data[1] != '4':
-									print(sam2tab(data))
-					else:
-						if options.type == 'sam':
-							print('\t'.join(data))
-						else:
-							if data[1] != '4':
-								print(sam2tab(data))
-			else:
-				if options.type == 'sam':
-					print('\t'.join(data))
-
-if __name__ == "__main__": __main__()
-
-
-
+#!/usr/bin/env python
+# -*- coding:Utf-8 -*-
+
+#
+#  Copyright 2014 CIRAD
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, see <http://www.gnu.org/licenses/> or
+#  write to the Free Software Foundation, Inc.,
+#  51 Franklin Street, Fifth Floor, Boston,
+#  MA 02110-1301, USA.
+#
+#
+
+
+import optparse, os, shutil, subprocess, sys, tempfile, fileinput, ConfigParser, operator, time
+
+
+def find_info(LINE):
+	dic = {}
+	for n in LINE[11:]:
+		liste = n.split(':')
+		if len(liste) > 2:
+			dic[liste[0]] = liste[2]
+	return dic
+
+def CIGAR(mot):
+	if 'N' in mot:
+		sys.exit('N in mot')
+	elif 'P' in mot:
+		sys.exit('P in mot')
+	elif '=' in mot:
+		sys.exit('= in mot')
+	elif 'X' in mot:
+		sys.exit('X in mot')
+	else:
+		mot_split = mot.replace('M',' M ').replace('D',' D ').replace('I',' I ').replace('S',' S ').replace('H',' H ').split()
+	total = 0
+	while mot_split:
+		if mot_split[1] == 'M' or mot_split[1] == 'D':
+			total = total + int(mot_split[0])
+		del mot_split[0]
+		del mot_split[0]
+	return total
+
+def sam2tab(LINE):
+	TOTAL = CIGAR(LINE[5])
+	if LINE[1] == '0':
+		return LINE[0]+'\t'+LINE[2]+'\t-\t1\t-\t'+LINE[3]+'\t'+str(int(LINE[3])+TOTAL)+'\t1'
+	elif LINE[1] == '16':
+		return LINE[0]+'\t'+LINE[2]+'\t-\t1\t-\t'+LINE[3]+'\t'+str(int(LINE[3])+TOTAL)+'\t-1'
+	else:
+		sys.exit('Probleme in sam flag '+LINE[1])
+
+def __main__():
+	#Parse Command Line
+	parser = optparse.OptionParser(usage="python %prog [options]\n\nProgram designed by Guillaume MARTIN : [email protected]")
+	# Wrapper options. 
+	parser.add_option( '', '--sam', dest='sam', help='The sam file')
+	parser.add_option( '', '--dif', dest='dif', help='The minimal difference between the best and second hit accepted to consider the hit as single')
+	parser.add_option( '', '--type', dest='type', help='The output type, sam or tab')
+	(options, args) = parser.parse_args()
+
+	min_dif = int(options.dif)
+
+	file = open(options.sam)
+	if options.type != 'sam' and options.type != 'tab':
+		sys.exit('Output option is not recognised')
+	for line in file:
+		data = line.split()
+		if data:
+			if data[0][0] != '@':
+				if data[1] != '256' and data[1] != '272':
+					dico = find_info(data)
+					if 'XS' in dico:
+						if abs(int(dico['AS'])-int(dico['XS'])) >= min_dif:
+							if options.type == 'sam':
+								print('\t'.join(data))
+							else:
+								if data[1] != '4':
+									print(sam2tab(data))
+					else:
+						if options.type == 'sam':
+							print('\t'.join(data))
+						else:
+							if data[1] != '4':
+								print(sam2tab(data))
+			else:
+				if options.type == 'sam':
+					print('\t'.join(data))
+
+if __name__ == "__main__": __main__()
+
+
+