X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Flowercase_seq;h=16158e9c654d15a573d8f31a89cc2df650915759;hb=48bea5c28b89dc5586d0bddb338ccd6ba23aa1f9;hp=b51df83a5ebb2007de9e86f866a71c2202c1fc84;hpb=e8e32d43d674573ff4a66fe77780cc18cb02d430;p=biopieces.git

diff --git a/bp_bin/lowercase_seq b/bp_bin/lowercase_seq
deleted file mode 100755
index b51df83..0000000
--- a/bp_bin/lowercase_seq
+++ /dev/null
@@ -1,178 +0,0 @@
-#!/usr/bin/python
-
-import os, string, sys, getopt, Args, optparse
-
-record_delimiter = "\n---\n"
-
-class Lowercase_seq:
-	in_stream = None
-	out_stream = None
-	eo_buffer = False
-	buffer = ''
-	rec_dic = {}
-	rec_num = 0
-
-	###########################################
-	def __init__(self):
-		pass
-	###########################################
-
-	###########################################
-	def open_streams(self, input_file, output_file):
-		#print input_file, output_file
-		if input_file == '':
-			self.in_stream = sys.stdin
-			#print "in_stream = <STDIN>"
-		else:
-			try:
-				self.in_stream = open(input_file, 'r')
-				#print "in_stream = %s" % (input_file)
-			except:
-				raise IOError
-
-		if output_file == '':
-			self.out_stream = sys.stdout
-			#print "out_stream = <STDOUT>"
-		else:
-			try:
-				self.out_stream = open(output_file, 'w')
-				#print "out_stream = %s" % (output_file)
-			except:
-				raise IOError
-	###########################################
-
-	###########################################
-	def close_streams(self):
-		if self.in_stream:
-			self.in_stream.close()
-		if self.out_stream:
-			self.out_stream.close()
-	###########################################
-
-	###########################################
-	def get_record(self):
-		rec = ''
-		eof_flag = False
-		while not self.eo_buffer:
-			#print "STDIN.ISATTY :", self.in_stream.isatty()
-
-			if self.in_stream.isatty():
-				eof_flag = True
-
-			if eof_flag:
-				if self.buffer == '':
-					self.eo_buffer = True
-					break
-			else:
-				tmp = self.in_stream.read(1000)
-			if not tmp:
-				eof_flag = True
-
-			self.buffer = self.buffer + tmp
-			delim_index = self.buffer.find(record_delimiter)
-			if delim_index >= 0:
-				rec = self.buffer[:delim_index]
-				self.buffer = self.buffer[delim_index + len(record_delimiter):]
-				break
-		return rec
-	###########################################
-
-	###########################################
-	def process_record(self, rec):
-		#print "PARSE_RECORD"
-		#print rec
-		#print "==="
-		lines = rec.split("\n")
-		self.rec_num += 1
-		self.rec_dic[self.rec_num] = {}
-		for l in lines:
-			toks = l.split(": ")
-			if toks[0]=="SEQ":
-				self.rec_dic[self.rec_num][toks[0]] = toks[1].lower()
-			else:
-				self.rec_dic[self.rec_num][toks[0]] = toks[1]
-			#self.rec_dic[self.rec_num][toks[0]] = toks[1]
-		#print self.rec_dic[self.rec_num]
-		return self.rec_num
-	###########################################
-
-	###########################################
-	def put_record(self, r_num):
-		rec = self.rec_dic[r_num]
-		for k in rec.keys():
-			#print "%s: %s" % (k, rec[k])
-			self.out_stream.write("%s: %s\n" % (k, rec[k]))
-		#print "---"
-		self.out_stream.write("---\n")
-	###########################################
-
-	###########################################
-	def print_usage(self, opt):
-		#print opt
-		bp_dir = os.environ['BP_DIR']
-		usage_path = bp_dir + os.path.sep + "bp_usage" + os.path.sep + "lowercase_seq.wiki"
-		os.system("print_usage -i %s %s" % (usage_path, opt))
-	###########################################
-
-
-# main
-
-lc_seq = Lowercase_seq()
-
-try:
-	opts, args = getopt.getopt(sys.argv[1:], "I:O:?vx", ["stream_in=", "stream_out=", "help", "verbose", "no_stream"])
-except getopt.GetoptError, err:
-	# print help information and exit:
-	print str(err) # will print something like "option -a not recognized"
-	lc_seq.print_usage("")
-	sys.exit(2)
-
-
-if len(opts)==0:
-	lc_seq.print_usage("")
-	sys.exit(1)
-
-stream_in = ""
-stream_out = ""
-verbose = False
-for o, a in opts:
-	if o in ("-I", "--stream_in"):
-		stream_in = a
-	elif o in ("-O", "--stream_out"):
-		stream_out = a
-	elif o == "-?":
-		lc_seq.print_usage("")
-		sys.exit(1)
-	elif o == "--help":
-		lc_seq.print_usage("-?")
-		sys.exit(1)
-	elif o in ("-v", "--verbose"):
-		verbose = True
-	#else:
-	#	assert False
-	#	print_usage()
-
-try:
-	lc_seq.open_streams(stream_in, stream_out)
-except:
-	sys.stderr.write("%s\n" % ("IOError"))
-	sys.exit(1)
-
-
-while True:
-	rec = lc_seq.get_record()
-	if rec=='':
-		break
-	rec_num = lc_seq.process_record(rec)
-	lc_seq.put_record(rec_num)
-
-lc_seq.close_streams()
-
-#source = "Dmel_tRNAs_key_record_tuples.txt"
-#lc_seq.open_stream(source)
-
-#lc_seq.get_record()
-#lc_seq.put_record()
-
-
-
diff --git a/bp_bin/lowercase_seq b/bp_bin/lowercase_seq
new file mode 120000
index 0000000..16158e9
--- /dev/null
+++ b/bp_bin/lowercase_seq
@@ -0,0 +1 @@
+../code_python/Cjung/lowercase_seq
\ No newline at end of file