refactoring of assemble_pairs

[biopieces.git] / bp_bin / lowercase_seq

diff --git a/bp_bin/lowercase_seq b/bp_bin/lowercase_seq
deleted file mode 100755 (executable)
index b51df83a5ebb2007de9e86f866a71c2202c1fc84..0000000000000000000000000000000000000000
--- 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 (symlink)
index 0000000000000000000000000000000000000000..16158e9c654d15a573d8f31a89cc2df650915759
--- /dev/null
+++ b/bp_bin/lowercase_seq
@@ -0,0 +1 @@
+../code_python/Cjung/lowercase_seq
\ No newline at end of file