code_python/Cjung/lowercase_seq

   1 #!/usr/bin/python
   2
   3 import os, string, sys, getopt, Args
   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                         if eof_flag:
  58                                 if self.buffer == '':
  59                                         self.eo_buffer = True
  60                                         break
  61                         else:
  62                                 tmp = self.in_stream.read(1000)
  63                         if not tmp:
  64                                 eof_flag = True
  65
  66                         self.buffer = self.buffer + tmp
  67                         delim_index = self.buffer.find(record_delimiter)
  68                         if delim_index >= 0:
  69                                 rec = self.buffer[:delim_index]
  70                                 self.buffer = self.buffer[delim_index + len(record_delimiter):]
  71                                 break
  72                 return rec
  73         ###########################################
  74
  75         ###########################################
  76         def process_record(self, rec):
  77                 #print "PARSE_RECORD"
  78                 #print rec
  79                 #print "==="
  80                 lines = rec.split("\n")
  81                 self.rec_num += 1
  82                 self.rec_dic[self.rec_num] = {}
  83                 for l in lines:
  84                         toks = l.split(": ")
  85                         if toks[0]=="SEQ":
  86                                 self.rec_dic[self.rec_num][toks[0]] = toks[1].lower()
  87                         else:
  88                                 self.rec_dic[self.rec_num][toks[0]] = toks[1]
  89                         #self.rec_dic[self.rec_num][toks[0]] = toks[1]
  90                 #print self.rec_dic[self.rec_num]
  91                 return self.rec_num
  92         ###########################################
  93
  94         ###########################################
  95         def put_record(self, r_num):
  96                 rec = self.rec_dic[r_num]
  97                 for k in rec.keys():
  98                         #print "%s: %s" % (k, rec[k])
  99                         self.out_stream.write("%s: %s\n" % (k, rec[k]))
 100                 #print "---"
 101                 self.out_stream.write("---\n")
 102         ###########################################
 103
 104         ###########################################
 105         def print_usage(self, opt):
 106                 bp_dir = os.environ['BP_DIR']
 107                 usage_path = bp_dir + os.path.sep + "bp_usage" + os.path.sep + "lowercase_seq.wiki"
 108                 os.system("print_usage -i %s %s" % (usage_path, opt))
 109         ###########################################
 110
 111
 112 # main
 113
 114 """
 115 print "############"
 116 print len(sys.argv)
 117 print sys.argv
 118 print "############"
 119 """
 120
 121
 122 lc_seq = Lowercase_seq()
 123
 124 a = Args.Args('Usage: %(progname)s [-a value] [-b value] [-c] word [file...]')
 125
 126 a.opt['-I'] = ''    # input file
 127 a.opt['-O'] = ''    # output file
 128 a.getopt('I:O:?:v')                     # get user supplied option values
 129
 130 #print >> sys.stderr, a.opt
 131
 132 word = a.shift()                        # get the first of the remaining arguments
 133                                                         # use a.pop() to get the last instead
 134 if not word == None:
 135         sys.stderr.write("Unknown argument %s\n" % (word))
 136         sys.exit(1)
 137
 138 if sys.stdin.isatty():
 139         lc_seq.print_usage('')
 140         sys.exit(1)
 141
 142 #for line in a:              # iterate over the contents of all remaining arguments (file names)
 143 #       if a.lineno == 1:
 144 #               print 'starting new file:', a.infile
 145 #       a.warning(line.rstrip())
 146
 147 #print 'Options:', a.opt
 148 #print 'Word:', word
 149 #print 'Total number of lines:', a.linesum
 150
 151
 152 if a.opt.has_key('-?'):
 153         lc_seq.print_usage('-?')
 154         sys.exit(1)
 155 else:
 156         try:
 157                 lc_seq.open_streams(a.opt['-I'], a.opt['-O'])
 158         except:
 159                 sys.stderr.write("%s\n" % ("IOError"))
 160                 sys.exit(1)
 161
 162
 163 while True:
 164         rec = lc_seq.get_record()
 165         if rec=='':
 166                 break
 167         rec_num = lc_seq.process_record(rec)
 168         lc_seq.put_record(rec_num)
 169
 170 lc_seq.close_streams()
 171
 172 #source = "Dmel_tRNAs_key_record_tuples.txt"
 173 #lc_seq.open_stream(source)
 174
 175 #lc_seq.get_record()
 176 #lc_seq.put_record()
 177
 178
 179