git.donarmstrong.com Git - biopieces.git/blob - code_python/Cjung/lowercase

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