bp_bin/lowercase_seq

   1 #!/usr/bin/python
   2
   3 import os, string, sys, getopt, Args, optparse
   4
   5 record_delimiter = "\n---\n"
   6
   7 class Lowercase_seq:
   8         in_stream = None
   9         out_stream = None
  10         eo_buffer = False
  11         buffer = ''
  12         rec_dic = {}
  13         rec_num = 0
  14
  15         ###########################################
  16         def __init__(self):
  17                 pass
  18         ###########################################
  19
  20         ###########################################
  21         def open_streams(self, input_file, output_file):
  22                 #print input_file, output_file
  23                 if input_file == '':
  24                         self.in_stream = sys.stdin
  25                         #print "in_stream = <STDIN>"
  26                 else:
  27                         try:
  28                                 self.in_stream = open(input_file, 'r')
  29                                 #print "in_stream = %s" % (input_file)
  30                         except:
  31                                 raise IOError
  32
  33                 if output_file == '':
  34                         self.out_stream = sys.stdout
  35                         #print "out_stream = <STDOUT>"
  36                 else:
  37                         try:
  38                                 self.out_stream = open(output_file, 'w')
  39                                 #print "out_stream = %s" % (output_file)
  40                         except:
  41                                 raise IOError
  42         ###########################################
  43
  44         ###########################################
  45         def close_streams(self):
  46                 if self.in_stream:
  47                         self.in_stream.close()
  48                 if self.out_stream:
  49                         self.out_stream.close()
  50         ###########################################
  51
  52         ###########################################
  53         def get_record(self):
  54                 rec = ''
  55                 eof_flag = False
  56                 while not self.eo_buffer:
  57                         #print "STDIN.ISATTY :", self.in_stream.isatty()
  58
  59                         if self.in_stream.isatty():
  60                                 eof_flag = True
  61
  62                         if eof_flag:
  63                                 if self.buffer == '':
  64                                         self.eo_buffer = True
  65                                         break
  66                         else:
  67                                 tmp = self.in_stream.read(1000)
  68                         if not tmp:
  69                                 eof_flag = True
  70
  71                         self.buffer = self.buffer + tmp
  72                         delim_index = self.buffer.find(record_delimiter)
  73                         if delim_index >= 0:
  74                                 rec = self.buffer[:delim_index]
  75                                 self.buffer = self.buffer[delim_index + len(record_delimiter):]
  76                                 break
  77                 return rec
  78         ###########################################
  79
  80         ###########################################
  81         def process_record(self, rec):
  82                 #print "PARSE_RECORD"
  83                 #print rec
  84                 #print "==="
  85                 lines = rec.split("\n")
  86                 self.rec_num += 1
  87                 self.rec_dic[self.rec_num] = {}
  88                 for l in lines:
  89                         toks = l.split(": ")
  90                         if toks[0]=="SEQ":
  91                                 self.rec_dic[self.rec_num][toks[0]] = toks[1].lower()
  92                         else:
  93                                 self.rec_dic[self.rec_num][toks[0]] = toks[1]
  94                         #self.rec_dic[self.rec_num][toks[0]] = toks[1]
  95                 #print self.rec_dic[self.rec_num]
  96                 return self.rec_num
  97         ###########################################
  98
  99         ###########################################
 100         def put_record(self, r_num):
 101                 rec = self.rec_dic[r_num]
 102                 for k in rec.keys():
 103                         #print "%s: %s" % (k, rec[k])
 104                         self.out_stream.write("%s: %s\n" % (k, rec[k]))
 105                 #print "---"
 106                 self.out_stream.write("---\n")
 107         ###########################################
 108
 109         ###########################################
 110         def print_usage(self, opt):
 111                 #print opt
 112                 bp_dir = os.environ['BP_DIR']
 113                 usage_path = bp_dir + os.path.sep + "bp_usage" + os.path.sep + "lowercase_seq.wiki"
 114                 os.system("print_usage -i %s %s" % (usage_path, opt))
 115         ###########################################
 116
 117
 118 # main
 119
 120 lc_seq = Lowercase_seq()
 121
 122 try:
 123         opts, args = getopt.getopt(sys.argv[1:], "I:O:?vx", ["stream_in=", "stream_out=", "help", "verbose", "no_stream"])
 124 except getopt.GetoptError, err:
 125         # print help information and exit:
 126         print str(err) # will print something like "option -a not recognized"
 127         lc_seq.print_usage("")
 128         sys.exit(2)
 129
 130
 131 if len(opts)==0:
 132         lc_seq.print_usage("")
 133         sys.exit(1)
 134
 135 stream_in = ""
 136 stream_out = ""
 137 verbose = False
 138 for o, a in opts:
 139         if o in ("-I", "--stream_in"):
 140                 stream_in = a
 141         elif o in ("-O", "--stream_out"):
 142                 stream_out = a
 143         elif o == "-?":
 144                 lc_seq.print_usage("")
 145                 sys.exit(1)
 146         elif o == "--help":
 147                 lc_seq.print_usage("-?")
 148                 sys.exit(1)
 149         elif o in ("-v", "--verbose"):
 150                 verbose = True
 151         #else:
 152         #       assert False
 153         #       print_usage()
 154
 155 try:
 156         lc_seq.open_streams(stream_in, stream_out)
 157 except:
 158         sys.stderr.write("%s\n" % ("IOError"))
 159         sys.exit(1)
 160
 161
 162 while True:
 163         rec = lc_seq.get_record()
 164         if rec=='':
 165                 break
 166         rec_num = lc_seq.process_record(rec)
 167         lc_seq.put_record(rec_num)
 168
 169 lc_seq.close_streams()
 170
 171 #source = "Dmel_tRNAs_key_record_tuples.txt"
 172 #lc_seq.open_stream(source)
 173
 174 #lc_seq.get_record()
 175 #lc_seq.put_record()
 176
 177
 178