diff data_stores/fasta_format.py @ 1:5c5027485f7d draft

Uploaded correct file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_stores/fasta_format.py	Sun Aug 09 16:07:50 2015 -0400
@@ -0,0 +1,195 @@
+#!/usr/bin/python		
+# Simple comparison and conversion tools for big fasta data
+
+import sys, os, optparse
+
+VERSION = "1.0.0"
+
+class MyParser(optparse.OptionParser):
+	"""
+	Provides a better class for displaying formatted help info.
+	From http://stackoverflow.com/questions/1857346/python-optparse-how-to-include-additional-info-in-usage-output.
+	"""
+	def format_epilog(self, formatter):
+		return self.epilog
+
+
+def split_len(seq, length):
+	return [seq[i:i+length] for i in range(0, len(seq), length)]
+
+
+def check_file_path(file_path, message = "File "):
+		
+	path = os.path.normpath(file_path)
+	# make sure any relative paths are converted to absolute ones
+	if not os.path.isdir(os.path.dirname(path)) or not os.path.isfile(path): 
+		# Not an absolute path, so try default folder where script was called:
+		path = os.path.normpath(os.path.join(os.getcwd(), path) )
+		if not os.path.isfile(path):
+			print message + "[" + file_path + "] doesn't exist!"
+			sys.exit(1)
+
+	return path
+		
+
+class FastaFormat(object):
+
+	def __main__(self):
+
+		options, args = self.get_command_line()
+
+		if options.code_version:
+			print VERSION
+			return VERSION
+	
+		if len(args) > 0:
+			file_a = check_file_path(args[0])
+		else: file_a = False
+		
+		if len(args) > 1:
+			file_b = check_file_path(args[1])
+		else: file_b = False			
+
+		if options.to_fasta == True:
+			# Transform from key-value file to regular fasta format: 1 line for identifier and description(s), remaining 80 character lines for fasta data.
+
+			with sys.stdout as outputFile :
+				for line in open(file_a,'r') if file_a else sys.stdin:
+					line_data =	line.rsplit('\t',1)
+					if len(line_data) > 1:
+						outputFile.write(line_data[0] + '\n' + '\n'.join(split_len(line_data[1],80)) )
+					else:
+						# Fasta one-liner didn't have any sequence data
+						outputFile.write(line_data[0])
+					
+			#outputFile.close() 	#Otherwise terminal never looks like it closes?
+	
+	
+		elif options.to_keyvalue == True:	
+			# Transform from fasta format to key-value format:
+			# Separates sequence lines are merged and separated from id/description line by a tab.
+			with sys.stdout as outputFile:
+				start = True
+				for line in open(file_a,'r') if file_a else sys.stdin:
+					if line[0] == ">":
+						if start == False:
+							outputFile.write('\n')
+						else:
+							start = False
+						outputFile.write(line.strip() + '\t')
+
+					else:
+						outputFile.write(line.strip())	
+
+
+		elif options.compare == True:
+
+			if len(args) < 2:
+				print "Error: Need two fasta file paths to compare"
+				sys.exit(1)
+			
+			file_a = open(file_a,'r')
+			file_b = open(file_b,'r')
+
+			p = 3 
+			count_a = 0
+			count_b = 0
+			sample_length = 50
+
+			while True: 
+
+				if p&1: 
+					a = file_a.readline() 
+					count_a += 1
+
+				if p&2: 
+					b = file_b.readline() 
+					count_b += 1
+		
+				if not a or not b: # blank line still has "cr\lf" in it so doesn't match here 
+					print "EOF"
+					break 
+
+				a = a.strip() 
+				b = b.strip()
+		
+				if a == b: 
+					p = 3 
+		
+				elif a < b: 
+					sys.stdout.write('f1 ln %s: -%s\nvs.   %s \n' % (count_a, a[0:sample_length] , b[0:sample_length])) 
+					p = 1 
+		
+				else: 
+					sys.stdout.write('f2 ln %s: +%s\nvs.   %s \n' % (count_b, b[0:sample_length] , a[0:sample_length]))
+					p = 2 
+
+	
+				if count_a % 1000000 == 0:
+					print "At line %s:" % count_a
+
+				# For testing:
+				#if count_a > 50:
+				#	
+				#	print "Quick exit at line 500"
+				#	sys.exit(1)
+	
+
+			for line in file_a.readlines(): 
+				count_a += 1
+				sys.stdout.write('f1 ln %s: -%s\nvs.   %s \n' % (count_a, line[0:sample_length] )) 
+
+			for line in file_b.readlines():
+				count_b += 1 
+				sys.stdout.write('f2 ln %s: +%s\nvs.   %s \n' % (count_b, line[0:sample_length] )) 
+
+		
+		
+
+	def get_command_line(self):
+		"""
+		*************************** Parse Command Line *****************************
+	
+		"""
+		parser = MyParser(
+			description = 'Tool for comparing two fasta files, or transforming fasta data to single-line key-value format, or visa versa.',
+			usage = 'fasta_format.py [options]',
+			epilog="""
+	Note: This tool uses stdin and stdout for transforming fasta data.
+			
+	Convert from key-value data to fasta format data:
+		fasta_format.py [file] -f --fasta 
+		cat [file] | fasta_format.py -f --fasta 
+		
+	Convert from fasta format data to key-value data:	
+		fasta_format.py [file] -k --keyvalue 
+		cat [file] | fasta_format.py -k --keyvalue 
+
+	Compare two fasta format files:	
+		fasta_format.py [file1] [file2] -c --compare 
+
+	Return version of this code:	
+		fasta_format.py -v --version 		
+
+""")
+
+		parser.add_option('-c', '--compare', dest='compare', default=False, action='store_true', 
+			help='Compare two fasta files')
+
+		parser.add_option('-f', '--fasta', dest='to_fasta', default=False, action='store_true', 
+			help='Transform key-value file to fasta file format')
+
+		parser.add_option('-k', '--keyvalue', dest='to_keyvalue', default=False, action='store_true', 
+			help='Transform fasta file format to key-value format')
+
+		parser.add_option('-v', '--version', dest='code_version', default=False, action='store_true', 
+			help='Return version of this code.')
+
+		return parser.parse_args()
+	
+
+if __name__ == '__main__':
+
+	fasta_format = FastaFormat()
+	fasta_format.__main__()
+