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1 #!/usr/bin/python
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2
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3 import sys
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4 import os
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5 import os.path
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6 import re
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7
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8 # Define the Dictionary & the Reverse Dictionary for barcode
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9
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10 # ===========================================
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11 #
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12 def FilterFastq (infile, outfile) :
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13 try:
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14 INFILE = open(infile, 'r')
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15 except IOError:
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16 print "\n[Error]:\n\t File cannot be open: ", infile;
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17 exit(-1)
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18 try:
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19 OUTFILE = open(outfile, 'w')
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20 except IOError:
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21 print "\n[Error]:\n\t File cannot be open: ", outfile;
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22 exit(-1)
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23 Dict = {}
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24 count = 0
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25 total = 0
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26 while 1 :
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27 line1 = INFILE.readline()
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28 if not line1 :
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29 break
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30 line1 = line1
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31 line2 = INFILE.readline()
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32 line3 = INFILE.readline()
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33 line4 = INFILE.readline()
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34 total += 1
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35 # print line2
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36 if ( line2 in Dict ) :
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37 Dict[line2] += 1
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38 else :
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39 Dict[line2] = 1
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40 OUTFILE.write(line1)
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41 OUTFILE.write(line2)
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42 OUTFILE.write(line3)
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43 OUTFILE.write(line4)
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44 count += 1
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45 INFILE.close()
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46 OUTFILE.close()
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47 print "Count of total raw reads: ", total
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48 print "Count of reads left: ", count
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49 print "Percentage of kept reads: %.2f" % (count * 100.0 /total), "%"
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50
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51
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52 # ===============================
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53 #
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54
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55 def FilterSequence (infile, outfile) :
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56 try:
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57 INFILE = open(infile, 'r')
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58 except IOError:
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59 print "\n[Error]:\n\t File cannot be open: ", infile;
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60 exit(-1)
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61 try:
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62 OUTFILE = open(outfile, 'w')
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63 except IOError:
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64 print "\n[Error]:\n\t File cannot be open: ", outfile;
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65 exit(-1)
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66 Dict = {}
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67 count = 0
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68 total = 0
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69 for line in INFILE:
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70 line = line.strip()
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71 total += 1
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72 if ( line in Dict ) :
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73 Dict[line] += 1
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74 else :
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75 Dict[line] = 1
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76 count += 1
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77 OUTFILE.write(line + "\n")
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78 INFILE.close()
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79 OUTFILE.close()
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80 print "Count of total raw reads: ", total
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81 print "Count of reads left: ", count
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82 print "Percentage of kept reads: %.2f" % (count * 100.0 /total), "%"
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83
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84 # ===============================
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85 # SN603 WA047 6 1101 41.40 99.10 0 1 .GGGA.......TTAG.............. @SZ__@@@@@@@RR__@@@@@@@@@@@@@@ 0
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86 #
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87 def FilterQseq (infile, outfile, keepquality) :
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88 if keepquality :
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89 print "User specified '-k' and read quality will not be considered"
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90 else :
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91 print "Reads with PF=0 will be filtered"
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92
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93 try:
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94 INFILE = open(infile, 'r')
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95 except IOError:
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96 print "\n[Error]:\n\t File cannot be open: ", infile;
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97 exit(-1)
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98 try:
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99 OUTFILE = open(outfile, 'w')
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100 except IOError:
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101 print "\n[Error]:\n\t File cannot be open: ", outfile;
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102 exit(-1)
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103 Dict = {}
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104 count = 0
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105 total = 0
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106 for line in INFILE:
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107 tokens = line.strip().split()
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108 total += 1
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109 if ( (not keepquality and tokens[10] == "1") or keepquality ) :
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110 if ( tokens[8] in Dict ) :
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111 Dict[tokens[8]] += 1
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112 else :
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113 Dict[tokens[8]] = 1
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114 count += 1
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115 OUTFILE.write(line)
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116
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117 INFILE.close()
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118 OUTFILE.close()
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119 print "Count of total raw reads: ", total
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120 print "Count of reads left: ", count
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121 print "Percentage of kept reads: %.2f" % (count * 100.0 /total), "%"
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122
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123
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124 # ===============================
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125 #
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126
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127 def FilterFasta (infile, outfile) :
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128 try:
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129 INFILE = open(infile, 'r')
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130 except IOError:
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131 print "\n[Error]:\n\t File cannot be open: ", infile;
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132 exit(-1)
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133 try:
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134 OUTFILE = open(outfile, 'w')
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135 except IOError:
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136 print "\n[Error]:\n\t File cannot be open: ", outfile;
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137 exit(-1)
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138 Dict = {}
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139 count = 0
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140 total = 0
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141 name = ""
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142 read = ""
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143 for line in INFILE:
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144 line = line.strip()
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145 if (line[0] == '>') :
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146 total += 1
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147 if ( name != "" ) :
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148 if ( read in Dict ) :
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149 Dict[read] += 1
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150 else :
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151 Dict[read] = 1
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152 count += 1
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153 OUTFILE.write(">" + name + "\n")
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154 OUTFILE.write(read + "\n")
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155 name = line[1:]
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156 read = ""
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157 else :
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158 read = read + line
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159 if (name != "") :
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160 if ( read in Dict ) :
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161 Dict[read] += 1
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162 else :
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163 Dict[read] = 1
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164 count += 1
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165 OUTFILE.write(">" + name + "\n")
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166 OUTFILE.write(read + "\n")
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167 print "Count of total raw reads: ", total
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168 print "Count of reads left: ", count
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169 print "Percentage of kept reads: %.2f" % (count * 100.0 /total), "%"
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170
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171
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172
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173 # ==============================
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174 # Decide branch functions for different format
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175
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176 def FilterReads (infile, outfile, keepquality):
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177 try:
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178 INFILE = open(infile, 'r')
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179 except IOError:
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180 print "\n[Error]:\n\t File cannot be open: ", infile;
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181 exit(-1)
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182 i = 0
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183 # Count the numbers of barcodes in first 10000 lines
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184 line = INFILE.readline()
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185 tokens = line.strip().split()
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186 input_format="";
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187 if line[0]=="@" :
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188 input_format = "FastQ"
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189 n_fastq = 0
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190 elif len(tokens) == 1 and line[0] != ">":
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191 input_format = "sequence"
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192 elif len(tokens) == 11:
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193 input_format = "qseq"
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194 elif line[0]==">" :
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195 input_format = "fasta"
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196 INFILE.close()
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197
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198 print "Input file format detected: ", input_format
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199
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200 if input_format == "FastQ" :
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201 FilterFastq(infile, outfile)
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202 elif input_format == "sequence" :
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203 FilterSequence(infile, outfile)
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204 elif input_format == "qseq" :
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205 FilterQseq(infile, outfile, keepquality)
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206 elif input_format == "fasta" :
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207 FilterFasta(infile, outfile)
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208
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209
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210 from optparse import OptionParser
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211
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212 # ===========================================
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213 def main():
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214 usage = "Usage: %prog -i <input> -o <output> [-k]\n" \
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215 "Author : Guo, Weilong; guoweilong@gmail.com; 2012-11-10\n" \
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216 "Last Update: 2013-04-01" \
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217 "Description: Unique reads for qseq/fastq/fasta/sequencce,\n" \
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218 " and filter low quality reads in qseq file."
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219 parser = OptionParser(usage)
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220 parser.add_option("-i", dest="infile",
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221 help="Name of the input qseq/fastq/fasta/sequence file", metavar="FILE")
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222 parser.add_option("-o", dest="outfile",
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223 help="Name of the output file", metavar="FILE")
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224 parser.add_option("-k", dest="keepquality", default = False, action = "store_true",
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225 help="Would not filter low quality reads if specified")
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226 (options, args) = parser.parse_args()
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227
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228 if (options.infile is None) or (options.outfile is None) :
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229 print parser.print_help()
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230 exit(-1)
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231 FilterReads(options.infile, options.outfile, options.keepquality)
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232
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233
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234 # ===========================================
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235 if __name__ == "__main__":
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236 main()
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237
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