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How to use get_target_id method in autotest
Best Python code snippet using autotest_python
LienaEncoder.py
Source:LienaEncoder.py 
...42 bytes_to_send[4] = (data_type_lsb & 0xff000000) >> 2443 bytes_to_send[5] = (data_type_lsb & 0x00ff0000) >> 1644 bytes_to_send[6] = (data_type_lsb & 0x0000ff00) >> 845 bytes_to_send[7] = (data_type_lsb & 0x000000ff)46 bytes_to_send[8] = (message.get_target_id() & 0xff000000) >> 2447 bytes_to_send[9] = (message.get_target_id() & 0x00ff0000) >> 1648 bytes_to_send[10] = (message.get_target_id() & 0x0000ff00) >> 849 bytes_to_send[11] = (message.get_target_id() & 0x000000ff)50 bytes_to_send[12] = (message.get_origin_id() & 0xff000000) >> 2451 bytes_to_send[13] = (message.get_origin_id() & 0x00ff0000) >> 1652 bytes_to_send[14] = (message.get_origin_id() & 0x0000ff00) >> 853 bytes_to_send[15] = (message.get_origin_id() & 0x000000ff)54 bytes_to_send[16] = (message.get_timestamps() & 0xff00000000000000) >> 5655 bytes_to_send[17] = (message.get_timestamps() & 0x00ff000000000000) >> 4856 bytes_to_send[18] = (message.get_timestamps() & 0x0000ff0000000000) >> 4057 bytes_to_send[19] = (message.get_timestamps() & 0x000000ff00000000) >> 3258 bytes_to_send[20] = (message.get_timestamps() & 0x00000000ff000000) >> 2459 bytes_to_send[21] = (message.get_timestamps() & 0x0000000000ff0000) >> 1660 bytes_to_send[22] = (message.get_timestamps() & 0x000000000000ff00) >> 861 bytes_to_send[23] = (message.get_timestamps() & 0x00000000000000ff)62 bytes_to_send[24] = (message.get_dlc() & 0xff000000) >> 2463 bytes_to_send[25] = (message.get_dlc() & 0x00ff0000) >> 1664 bytes_to_send[26] = (message.get_dlc() & 0x0000ff00) >> 865 bytes_to_send[27] = (message.get_dlc() & 0x000000ff)66 body = message.get_message_body()67 for x in range(28, self.global_parameter.get_global_datagram_size()):68 bytes_to_send[x] = int(body[x-28])69 # print(int(bytes_to_send[40]), int(bytes_to_send[41]), int(bytes_to_send[42]), int(bytes_to_send[43]), int(bytes_to_send[44]), int(bytes_to_send[45]))70 datagram = LienaDatagram(self.global_parameter.get_global_datagram_size(), bytes_to_send)71 return datagram72 def encode_network_quality_message(self, message):73 bytes_to_send = bytearray(self.global_parameter.get_global_datagram_size())74 data_type_msb = message.get_message_id() // (2 ** 32)75 data_type_lsb = message.get_message_id() % (2 ** 32)76 bytes_to_send[0] = (data_type_msb & 0xff000000) >> 2477 bytes_to_send[1] = (data_type_msb & 0x00ff0000) >> 1678 bytes_to_send[2] = (data_type_msb & 0x0000ff00) >> 879 bytes_to_send[3] = (data_type_msb & 0x000000ff)80 bytes_to_send[4] = (data_type_lsb & 0xff000000) >> 2481 bytes_to_send[5] = (data_type_lsb & 0x00ff0000) >> 1682 bytes_to_send[6] = (data_type_lsb & 0x0000ff00) >> 883 bytes_to_send[7] = (data_type_lsb & 0x000000ff)84 bytes_to_send[8] = (message.get_target_id() & 0xff000000) >> 2485 bytes_to_send[9] = (message.get_target_id() & 0x00ff0000) >> 1686 bytes_to_send[10] = (message.get_target_id() & 0x0000ff00) >> 887 bytes_to_send[11] = (message.get_target_id() & 0x000000ff)88 bytes_to_send[12] = (message.get_origin_id() & 0xff000000) >> 2489 bytes_to_send[13] = (message.get_origin_id() & 0x00ff0000) >> 1690 bytes_to_send[14] = (message.get_origin_id() & 0x0000ff00) >> 891 bytes_to_send[15] = (message.get_origin_id() & 0x000000ff)92 bytes_to_send[16] = (message.get_timestamps() & 0xff00000000000000) >> 5693 bytes_to_send[17] = (message.get_timestamps() & 0x00ff000000000000) >> 4894 bytes_to_send[18] = (message.get_timestamps() & 0x0000ff0000000000) >> 4095 bytes_to_send[19] = (message.get_timestamps() & 0x000000ff00000000) >> 3296 bytes_to_send[20] = (message.get_timestamps() & 0x00000000ff000000) >> 2497 bytes_to_send[21] = (message.get_timestamps() & 0x0000000000ff0000) >> 1698 bytes_to_send[22] = (message.get_timestamps() & 0x000000000000ff00) >> 899 bytes_to_send[23] = (message.get_timestamps() & 0x00000000000000ff)100 bytes_to_send[24] = (message.get_dlc() & 0xff000000) >> 24101 bytes_to_send[25] = (message.get_dlc() & 0x00ff0000) >> 16102 bytes_to_send[26] = (message.get_dlc() & 0x0000ff00) >> 8103 bytes_to_send[27] = (message.get_dlc() & 0x000000ff)104 bytes_to_send[28] = message.get_index()105 bytes_to_send[29] = (message.get_t1() & 0xff00000000000000) >> 56106 bytes_to_send[30] = (message.get_t1() & 0x00ff000000000000) >> 48107 bytes_to_send[31] = (message.get_t1() & 0x0000ff0000000000) >> 40108 bytes_to_send[32] = (message.get_t1() & 0x000000ff00000000) >> 32109 bytes_to_send[33] = (message.get_t1() & 0x00000000ff000000) >> 24110 bytes_to_send[34] = (message.get_t1() & 0x0000000000ff0000) >> 16111 bytes_to_send[35] = (message.get_t1() & 0x000000000000ff00) >> 8112 bytes_to_send[36] = (message.get_t1() & 0x00000000000000ff)113 bytes_to_send[37] = (message.get_t2() & 0xff00000000000000) >> 56114 bytes_to_send[38] = (message.get_t2() & 0x00ff000000000000) >> 48115 bytes_to_send[39] = (message.get_t2() & 0x0000ff0000000000) >> 40116 bytes_to_send[40] = (message.get_t2() & 0x000000ff00000000) >> 32117 bytes_to_send[41] = (message.get_t2() & 0x00000000ff000000) >> 24118 bytes_to_send[42] = (message.get_t2() & 0x0000000000ff0000) >> 16119 bytes_to_send[43] = (message.get_t2() & 0x000000000000ff00) >> 8120 bytes_to_send[44] = (message.get_t2() & 0x00000000000000ff)121 bytes_to_send[45] = (message.get_t3() & 0xff00000000000000) >> 56122 bytes_to_send[46] = (message.get_t3() & 0x00ff000000000000) >> 48123 bytes_to_send[47] = (message.get_t3() & 0x0000ff0000000000) >> 40124 bytes_to_send[48] = (message.get_t3() & 0x000000ff00000000) >> 32125 bytes_to_send[49] = (message.get_t3() & 0x00000000ff000000) >> 24126 bytes_to_send[50] = (message.get_t3() & 0x0000000000ff0000) >> 16127 bytes_to_send[51] = (message.get_t3() & 0x000000000000ff00) >> 8128 bytes_to_send[52] = (message.get_t3() & 0x00000000000000ff)129 bytes_to_send[53] = (message.get_t4() & 0xff00000000000000) >> 56130 bytes_to_send[54] = (message.get_t4() & 0x00ff000000000000) >> 48131 bytes_to_send[55] = (message.get_t4() & 0x0000ff0000000000) >> 40132 bytes_to_send[56] = (message.get_t4() & 0x000000ff00000000) >> 32133 bytes_to_send[57] = (message.get_t4() & 0x00000000ff000000) >> 24134 bytes_to_send[58] = (message.get_t4() & 0x0000000000ff0000) >> 16135 bytes_to_send[59] = (message.get_t4() & 0x000000000000ff00) >> 8136 bytes_to_send[60] = (message.get_t4() & 0x00000000000000ff)137 for x in range(61, self.global_parameter.get_global_datagram_size()):138 bytes_to_send[x] = 0139 return bytes_to_send140 def encode_channel_reopened_message(self, message):141 bytes_to_send = bytearray(self.global_parameter.get_global_datagram_size())142 data_type_msb = message.get_message_id() // (2 ** 32)143 data_type_lsb = message.get_message_id() % (2 ** 32)144 bytes_to_send[0] = (data_type_msb & 0xff000000) >> 24145 bytes_to_send[1] = (data_type_msb & 0x00ff0000) >> 16146 bytes_to_send[2] = (data_type_msb & 0x0000ff00) >> 8147 bytes_to_send[3] = (data_type_msb & 0x000000ff)148 bytes_to_send[4] = (data_type_lsb & 0xff000000) >> 24149 bytes_to_send[5] = (data_type_lsb & 0x00ff0000) >> 16150 bytes_to_send[6] = (data_type_lsb & 0x0000ff00) >> 8151 bytes_to_send[7] = (data_type_lsb & 0x000000ff)152 bytes_to_send[8] = (message.get_target_id() & 0xff000000) >> 24153 bytes_to_send[9] = (message.get_target_id() & 0x00ff0000) >> 16154 bytes_to_send[10] = (message.get_target_id() & 0x0000ff00) >> 8155 bytes_to_send[11] = (message.get_target_id() & 0x000000ff)156 bytes_to_send[12] = (message.get_origin_id() & 0xff000000) >> 24157 bytes_to_send[13] = (message.get_origin_id() & 0x00ff0000) >> 16158 bytes_to_send[14] = (message.get_origin_id() & 0x0000ff00) >> 8159 bytes_to_send[15] = (message.get_origin_id() & 0x000000ff)160 bytes_to_send[16] = (message.get_timestamps() & 0xff00000000000000) >> 56161 bytes_to_send[17] = (message.get_timestamps() & 0x00ff000000000000) >> 48162 bytes_to_send[18] = (message.get_timestamps() & 0x0000ff0000000000) >> 40163 bytes_to_send[19] = (message.get_timestamps() & 0x000000ff00000000) >> 32164 bytes_to_send[20] = (message.get_timestamps() & 0x00000000ff000000) >> 24165 bytes_to_send[21] = (message.get_timestamps() & 0x0000000000ff0000) >> 16166 bytes_to_send[22] = (message.get_timestamps() & 0x000000000000ff00) >> 8167 bytes_to_send[23] = (message.get_timestamps() & 0x00000000000000ff)168 bytes_to_send[24] = (message.get_dlc() & 0xff000000) >> 24169 bytes_to_send[25] = (message.get_dlc() & 0x00ff0000) >> 16170 bytes_to_send[26] = (message.get_dlc() & 0x0000ff00) >> 8171 bytes_to_send[27] = (message.get_dlc() & 0x000000ff)172 for x in range(28, self.global_parameter.get_global_datagram_size()):173 bytes_to_send[x] = 0174 return bytes_to_send175 def encode_rehandshake_commit_message(self, message):176 bytes_to_send = bytearray(self.global_parameter.get_global_datagram_size())177 data_type_msb = message.get_message_id() // (2 ** 32)178 data_type_lsb = message.get_message_id() % (2 ** 32)179 bytes_to_send[0] = (data_type_msb & 0xff000000) >> 24180 bytes_to_send[1] = (data_type_msb & 0x00ff0000) >> 16181 bytes_to_send[2] = (data_type_msb & 0x0000ff00) >> 8182 bytes_to_send[3] = (data_type_msb & 0x000000ff)183 bytes_to_send[4] = (data_type_lsb & 0xff000000) >> 24184 bytes_to_send[5] = (data_type_lsb & 0x00ff0000) >> 16185 bytes_to_send[6] = (data_type_lsb & 0x0000ff00) >> 8186 bytes_to_send[7] = (data_type_lsb & 0x000000ff)187 bytes_to_send[8] = (message.get_target_id() & 0xff000000) >> 24188 bytes_to_send[9] = (message.get_target_id() & 0x00ff0000) >> 16189 bytes_to_send[10] = (message.get_target_id() & 0x0000ff00) >> 8190 bytes_to_send[11] = (message.get_target_id() & 0x000000ff)191 bytes_to_send[12] = (message.get_origin_id() & 0xff000000) >> 24192 bytes_to_send[13] = (message.get_origin_id() & 0x00ff0000) >> 16193 bytes_to_send[14] = (message.get_origin_id() & 0x0000ff00) >> 8194 bytes_to_send[15] = (message.get_origin_id() & 0x000000ff)195 bytes_to_send[16] = (message.get_timestamps() & 0xff00000000000000) >> 56196 bytes_to_send[17] = (message.get_timestamps() & 0x00ff000000000000) >> 48197 bytes_to_send[18] = (message.get_timestamps() & 0x0000ff0000000000) >> 40198 bytes_to_send[19] = (message.get_timestamps() & 0x000000ff00000000) >> 32199 bytes_to_send[20] = (message.get_timestamps() & 0x00000000ff000000) >> 24200 bytes_to_send[21] = (message.get_timestamps() & 0x0000000000ff0000) >> 16201 bytes_to_send[22] = (message.get_timestamps() & 0x000000000000ff00) >> 8202 bytes_to_send[23] = (message.get_timestamps() & 0x00000000000000ff)203 bytes_to_send[24] = (message.get_dlc() & 0xff000000) >> 24204 bytes_to_send[25] = (message.get_dlc() & 0x00ff0000) >> 16205 bytes_to_send[26] = (message.get_dlc() & 0x0000ff00) >> 8206 bytes_to_send[27] = (message.get_dlc() & 0x000000ff)207 for x in range(28, self.global_parameter.get_global_datagram_size()):208 bytes_to_send[x] = 0209 return bytes_to_send210 def encode_rehandshake_message(self, message):211 bytes_to_send = bytearray(self.global_parameter.get_global_datagram_size())212 data_type_msb = message.get_message_id() // (2 ** 32)213 data_type_lsb = message.get_message_id() % (2 ** 32)214 bytes_to_send[0] = (data_type_msb & 0xff000000) >> 24215 bytes_to_send[1] = (data_type_msb & 0x00ff0000) >> 16216 bytes_to_send[2] = (data_type_msb & 0x0000ff00) >> 8217 bytes_to_send[3] = (data_type_msb & 0x000000ff)218 bytes_to_send[4] = (data_type_lsb & 0xff000000) >> 24219 bytes_to_send[5] = (data_type_lsb & 0x00ff0000) >> 16220 bytes_to_send[6] = (data_type_lsb & 0x0000ff00) >> 8221 bytes_to_send[7] = (data_type_lsb & 0x000000ff)222 bytes_to_send[8] = (message.get_target_id() & 0xff000000) >> 24223 bytes_to_send[9] = (message.get_target_id() & 0x00ff0000) >> 16224 bytes_to_send[10] = (message.get_target_id() & 0x0000ff00) >> 8225 bytes_to_send[11] = (message.get_target_id() & 0x000000ff)226 bytes_to_send[12] = (message.get_origin_id() & 0xff000000) >> 24227 bytes_to_send[13] = (message.get_origin_id() & 0x00ff0000) >> 16228 bytes_to_send[14] = (message.get_origin_id() & 0x0000ff00) >> 8229 bytes_to_send[15] = (message.get_origin_id() & 0x000000ff)230 bytes_to_send[16] = (message.get_timestamps() & 0xff00000000000000) >> 56231 bytes_to_send[17] = (message.get_timestamps() & 0x00ff000000000000) >> 48232 bytes_to_send[18] = (message.get_timestamps() & 0x0000ff0000000000) >> 40233 bytes_to_send[19] = (message.get_timestamps() & 0x000000ff00000000) >> 32234 bytes_to_send[20] = (message.get_timestamps() & 0x00000000ff000000) >> 24235 bytes_to_send[21] = (message.get_timestamps() & 0x0000000000ff0000) >> 16236 bytes_to_send[22] = (message.get_timestamps() & 0x000000000000ff00) >> 8237 bytes_to_send[23] = (message.get_timestamps() & 0x00000000000000ff)238 bytes_to_send[24] = (message.get_dlc() & 0xff000000) >> 24239 bytes_to_send[25] = (message.get_dlc() & 0x00ff0000) >> 16240 bytes_to_send[26] = (message.get_dlc() & 0x0000ff00) >> 8241 bytes_to_send[27] = (message.get_dlc() & 0x000000ff)242 for x in range(28, self.global_parameter.get_global_datagram_size()):243 bytes_to_send[x] = 0244 return bytes_to_send245 def encode_channel_closed_message(self, message):246 bytes_to_send = bytearray(self.global_parameter.get_global_datagram_size())247 data_type_msb = message.get_message_id() // (2 ** 32)248 data_type_lsb = message.get_message_id() % (2 ** 32)249 bytes_to_send[0] = (data_type_msb & 0xff000000) >> 24250 bytes_to_send[1] = (data_type_msb & 0x00ff0000) >> 16251 bytes_to_send[2] = (data_type_msb & 0x0000ff00) >> 8252 bytes_to_send[3] = (data_type_msb & 0x000000ff)253 bytes_to_send[4] = (data_type_lsb & 0xff000000) >> 24254 bytes_to_send[5] = (data_type_lsb & 0x00ff0000) >> 16255 bytes_to_send[6] = (data_type_lsb & 0x0000ff00) >> 8256 bytes_to_send[7] = (data_type_lsb & 0x000000ff)257 bytes_to_send[8] = (message.get_target_id() & 0xff000000) >> 24258 bytes_to_send[9] = (message.get_target_id() & 0x00ff0000) >> 16259 bytes_to_send[10] = (message.get_target_id() & 0x0000ff00) >> 8260 bytes_to_send[11] = (message.get_target_id() & 0x000000ff)261 bytes_to_send[12] = (message.get_origin_id() & 0xff000000) >> 24262 bytes_to_send[13] = (message.get_origin_id() & 0x00ff0000) >> 16263 bytes_to_send[14] = (message.get_origin_id() & 0x0000ff00) >> 8264 bytes_to_send[15] = (message.get_origin_id() & 0x000000ff)265 bytes_to_send[16] = (message.get_timestamps() & 0xff00000000000000) >> 56266 bytes_to_send[17] = (message.get_timestamps() & 0x00ff000000000000) >> 48267 bytes_to_send[18] = (message.get_timestamps() & 0x0000ff0000000000) >> 40268 bytes_to_send[19] = (message.get_timestamps() & 0x000000ff00000000) >> 32269 bytes_to_send[20] = (message.get_timestamps() & 0x00000000ff000000) >> 24270 bytes_to_send[21] = (message.get_timestamps() & 0x0000000000ff0000) >> 16271 bytes_to_send[22] = (message.get_timestamps() & 0x000000000000ff00) >> 8272 bytes_to_send[23] = (message.get_timestamps() & 0x00000000000000ff)273 bytes_to_send[24] = (message.get_dlc() & 0xff000000) >> 24274 bytes_to_send[25] = (message.get_dlc() & 0x00ff0000) >> 16275 bytes_to_send[26] = (message.get_dlc() & 0x0000ff00) >> 8276 bytes_to_send[27] = (message.get_dlc() & 0x000000ff)277 for x in range(28, self.global_parameter.get_global_datagram_size()):278 bytes_to_send[x] = 0279 return bytes_to_send280 def encode_disengagement_commit_message(self, message):281 bytes_to_send = bytearray(self.global_parameter.get_global_datagram_size())282 data_type_msb = message.get_message_id() // (2 ** 32)283 data_type_lsb = message.get_message_id() % (2 ** 32)284 bytes_to_send[0] = (data_type_msb & 0xff000000) >> 24285 bytes_to_send[1] = (data_type_msb & 0x00ff0000) >> 16286 bytes_to_send[2] = (data_type_msb & 0x0000ff00) >> 8287 bytes_to_send[3] = (data_type_msb & 0x000000ff)288 bytes_to_send[4] = (data_type_lsb & 0xff000000) >> 24289 bytes_to_send[5] = (data_type_lsb & 0x00ff0000) >> 16290 bytes_to_send[6] = (data_type_lsb & 0x0000ff00) >> 8291 bytes_to_send[7] = (data_type_lsb & 0x000000ff)292 bytes_to_send[8] = (message.get_target_id() & 0xff000000) >> 24293 bytes_to_send[9] = (message.get_target_id() & 0x00ff0000) >> 16294 bytes_to_send[10] = (message.get_target_id() & 0x0000ff00) >> 8295 bytes_to_send[11] = (message.get_target_id() & 0x000000ff)296 bytes_to_send[12] = (message.get_origin_id() & 0xff000000) >> 24297 bytes_to_send[13] = (message.get_origin_id() & 0x00ff0000) >> 16298 bytes_to_send[14] = (message.get_origin_id() & 0x0000ff00) >> 8299 bytes_to_send[15] = (message.get_origin_id() & 0x000000ff)300 bytes_to_send[16] = (message.get_timestamps() & 0xff00000000000000) >> 56301 bytes_to_send[17] = (message.get_timestamps() & 0x00ff000000000000) >> 48302 bytes_to_send[18] = (message.get_timestamps() & 0x0000ff0000000000) >> 40303 bytes_to_send[19] = (message.get_timestamps() & 0x000000ff00000000) >> 32304 bytes_to_send[20] = (message.get_timestamps() & 0x00000000ff000000) >> 24305 bytes_to_send[21] = (message.get_timestamps() & 0x0000000000ff0000) >> 16306 bytes_to_send[22] = (message.get_timestamps() & 0x000000000000ff00) >> 8307 bytes_to_send[23] = (message.get_timestamps() & 0x00000000000000ff)308 bytes_to_send[24] = (message.get_dlc() & 0xff000000) >> 24309 bytes_to_send[25] = (message.get_dlc() & 0x00ff0000) >> 16310 bytes_to_send[26] = (message.get_dlc() & 0x0000ff00) >> 8311 bytes_to_send[27] = (message.get_dlc() & 0x000000ff)312 for x in range(28, self.global_parameter.get_global_datagram_size()):313 bytes_to_send[x] = 0314 return bytes_to_send315 def encode_disengagement_message(self, message):316 bytes_to_send = bytearray(self.global_parameter.get_global_datagram_size())317 data_type_msb = message.get_message_id() // (2 ** 32)318 data_type_lsb = message.get_message_id() % (2 ** 32)319 bytes_to_send[0] = (data_type_msb & 0xff000000) >> 24320 bytes_to_send[1] = (data_type_msb & 0x00ff0000) >> 16321 bytes_to_send[2] = (data_type_msb & 0x0000ff00) >> 8322 bytes_to_send[3] = (data_type_msb & 0x000000ff)323 bytes_to_send[4] = (data_type_lsb & 0xff000000) >> 24324 bytes_to_send[5] = (data_type_lsb & 0x00ff0000) >> 16325 bytes_to_send[6] = (data_type_lsb & 0x0000ff00) >> 8326 bytes_to_send[7] = (data_type_lsb & 0x000000ff)327 bytes_to_send[8] = (message.get_target_id() & 0xff000000) >> 24328 bytes_to_send[9] = (message.get_target_id() & 0x00ff0000) >> 16329 bytes_to_send[10] = (message.get_target_id() & 0x0000ff00) >> 8330 bytes_to_send[11] = (message.get_target_id() & 0x000000ff)331 bytes_to_send[12] = (message.get_origin_id() & 0xff000000) >> 24332 bytes_to_send[13] = (message.get_origin_id() & 0x00ff0000) >> 16333 bytes_to_send[14] = (message.get_origin_id() & 0x0000ff00) >> 8334 bytes_to_send[15] = (message.get_origin_id() & 0x000000ff)335 bytes_to_send[16] = (message.get_timestamps() & 0xff00000000000000) >> 56336 bytes_to_send[17] = (message.get_timestamps() & 0x00ff000000000000) >> 48337 bytes_to_send[18] = (message.get_timestamps() & 0x0000ff0000000000) >> 40338 bytes_to_send[19] = (message.get_timestamps() & 0x000000ff00000000) >> 32339 bytes_to_send[20] = (message.get_timestamps() & 0x00000000ff000000) >> 24340 bytes_to_send[21] = (message.get_timestamps() & 0x0000000000ff0000) >> 16341 bytes_to_send[22] = (message.get_timestamps() & 0x000000000000ff00) >> 8342 bytes_to_send[23] = (message.get_timestamps() & 0x00000000000000ff)343 bytes_to_send[24] = (message.get_dlc() & 0xff000000) >> 24344 bytes_to_send[25] = (message.get_dlc() & 0x00ff0000) >> 16345 bytes_to_send[26] = (message.get_dlc() & 0x0000ff00) >> 8346 bytes_to_send[27] = (message.get_dlc() & 0x000000ff)347 for x in range(28, self.global_parameter.get_global_datagram_size()):348 bytes_to_send[x] = 0349 return bytes_to_send350 def encode_handshake_commit_message(self, message):351 bytes_to_send = bytearray(self.global_parameter.get_global_datagram_size())352 data_type_msb = message.get_message_id() // (2 ** 32)353 data_type_lsb = message.get_message_id() % (2 ** 32)354 bytes_to_send[0] = (data_type_msb & 0xff000000) >> 24355 bytes_to_send[1] = (data_type_msb & 0x00ff0000) >> 16356 bytes_to_send[2] = (data_type_msb & 0x0000ff00) >> 8357 bytes_to_send[3] = (data_type_msb & 0x000000ff)358 bytes_to_send[4] = (data_type_lsb & 0xff000000) >> 24359 bytes_to_send[5] = (data_type_lsb & 0x00ff0000) >> 16360 bytes_to_send[6] = (data_type_lsb & 0x0000ff00) >> 8361 bytes_to_send[7] = (data_type_lsb & 0x000000ff)362 bytes_to_send[8] = (message.get_target_id() & 0xff000000) >> 24363 bytes_to_send[9] = (message.get_target_id() & 0x00ff0000) >> 16364 bytes_to_send[10] = (message.get_target_id() & 0x0000ff00) >> 8365 bytes_to_send[11] = (message.get_target_id() & 0x000000ff)366 bytes_to_send[12] = (message.get_origin_id() & 0xff000000) >> 24367 bytes_to_send[13] = (message.get_origin_id() & 0x00ff0000) >> 16368 bytes_to_send[14] = (message.get_origin_id() & 0x0000ff00) >> 8369 bytes_to_send[15] = (message.get_origin_id() & 0x000000ff)370 bytes_to_send[16] = (message.get_timestamps() & 0xff00000000000000) >> 56371 bytes_to_send[17] = (message.get_timestamps() & 0x00ff000000000000) >> 48372 bytes_to_send[18] = (message.get_timestamps() & 0x0000ff0000000000) >> 40373 bytes_to_send[19] = (message.get_timestamps() & 0x000000ff00000000) >> 32374 bytes_to_send[20] = (message.get_timestamps() & 0x00000000ff000000) >> 24375 bytes_to_send[21] = (message.get_timestamps() & 0x0000000000ff0000) >> 16376 bytes_to_send[22] = (message.get_timestamps() & 0x000000000000ff00) >> 8377 bytes_to_send[23] = (message.get_timestamps() & 0x00000000000000ff)378 bytes_to_send[24] = (message.get_dlc() & 0xff000000) >> 24379 bytes_to_send[25] = (message.get_dlc() & 0x00ff0000) >> 16380 bytes_to_send[26] = (message.get_dlc() & 0x0000ff00) >> 8381 bytes_to_send[27] = (message.get_dlc() & 0x000000ff)382 for x in range(28, self.global_parameter.get_global_datagram_size()):383 bytes_to_send[x] = 0384 return bytes_to_send385 def encode_heartbeat_message(self, message):386 bytes_to_send = bytearray(self.global_parameter.get_global_datagram_size())387 data_type_msb = message.get_message_id() // (2 ** 32)388 data_type_lsb = message.get_message_id() % (2 ** 32)389 bytes_to_send[0] = (data_type_msb & 0xff000000) >> 24390 bytes_to_send[1] = (data_type_msb & 0x00ff0000) >> 16391 bytes_to_send[2] = (data_type_msb & 0x0000ff00) >> 8392 bytes_to_send[3] = (data_type_msb & 0x000000ff)393 bytes_to_send[4] = (data_type_lsb & 0xff000000) >> 24394 bytes_to_send[5] = (data_type_lsb & 0x00ff0000) >> 16395 bytes_to_send[6] = (data_type_lsb & 0x0000ff00) >> 8396 bytes_to_send[7] = (data_type_lsb & 0x000000ff)397 bytes_to_send[8] = (message.get_target_id() & 0xff000000) >> 24398 bytes_to_send[9] = (message.get_target_id() & 0x00ff0000) >> 16399 bytes_to_send[10] = (message.get_target_id() & 0x0000ff00) >> 8400 bytes_to_send[11] = (message.get_target_id() & 0x000000ff)401 bytes_to_send[12] = (message.get_origin_id() & 0xff000000) >> 24402 bytes_to_send[13] = (message.get_origin_id() & 0x00ff0000) >> 16403 bytes_to_send[14] = (message.get_origin_id() & 0x0000ff00) >> 8404 bytes_to_send[15] = (message.get_origin_id() & 0x000000ff)405 bytes_to_send[16] = (message.get_timestamps() & 0xff00000000000000) >> 56406 bytes_to_send[17] = (message.get_timestamps() & 0x00ff000000000000) >> 48407 bytes_to_send[18] = (message.get_timestamps() & 0x0000ff0000000000) >> 40408 bytes_to_send[19] = (message.get_timestamps() & 0x000000ff00000000) >> 32409 bytes_to_send[20] = (message.get_timestamps() & 0x00000000ff000000) >> 24410 bytes_to_send[21] = (message.get_timestamps() & 0x0000000000ff0000) >> 16411 bytes_to_send[22] = (message.get_timestamps() & 0x000000000000ff00) >> 8412 bytes_to_send[23] = (message.get_timestamps() & 0x00000000000000ff)413 bytes_to_send[24] = (message.get_dlc() & 0xff000000) >> 24414 bytes_to_send[25] = (message.get_dlc() & 0x00ff0000) >> 16415 bytes_to_send[26] = (message.get_dlc() & 0x0000ff00) >> 8416 bytes_to_send[27] = (message.get_dlc() & 0x000000ff)417 for x in range(28, self.global_parameter.get_global_datagram_size()):418 bytes_to_send[x] = 0419 return bytes_to_send420 def encode_channelopened_message(self, message):421 bytes_to_send = bytearray(self.global_parameter.get_global_datagram_size())422 data_type_msb = message.get_message_id() // (2 ** 32)423 data_type_lsb = message.get_message_id() % (2 ** 32)424 bytes_to_send[0] = (data_type_msb & 0xff000000) >> 24425 bytes_to_send[1] = (data_type_msb & 0x00ff0000) >> 16426 bytes_to_send[2] = (data_type_msb & 0x0000ff00) >> 8427 bytes_to_send[3] = (data_type_msb & 0x000000ff)428 bytes_to_send[4] = (data_type_lsb & 0xff000000) >> 24429 bytes_to_send[5] = (data_type_lsb & 0x00ff0000) >> 16430 bytes_to_send[6] = (data_type_lsb & 0x0000ff00) >> 8431 bytes_to_send[7] = (data_type_lsb & 0x000000ff)432 bytes_to_send[8] = (message.get_target_id() & 0xff000000) >> 24433 bytes_to_send[9] = (message.get_target_id() & 0x00ff0000) >> 16434 bytes_to_send[10] = (message.get_target_id() & 0x0000ff00) >> 8435 bytes_to_send[11] = (message.get_target_id() & 0x000000ff)436 bytes_to_send[12] = (message.get_origin_id() & 0xff000000) >> 24437 bytes_to_send[13] = (message.get_origin_id() & 0x00ff0000) >> 16438 bytes_to_send[14] = (message.get_origin_id() & 0x0000ff00) >> 8439 bytes_to_send[15] = (message.get_origin_id() & 0x000000ff)440 bytes_to_send[16] = (message.get_timestamps() & 0xff00000000000000) >> 56441 bytes_to_send[17] = (message.get_timestamps() & 0x00ff000000000000) >> 48442 bytes_to_send[18] = (message.get_timestamps() & 0x0000ff0000000000) >> 40443 bytes_to_send[19] = (message.get_timestamps() & 0x000000ff00000000) >> 32444 bytes_to_send[20] = (message.get_timestamps() & 0x00000000ff000000) >> 24445 bytes_to_send[21] = (message.get_timestamps() & 0x0000000000ff0000) >> 16446 bytes_to_send[22] = (message.get_timestamps() & 0x000000000000ff00) >> 8447 bytes_to_send[23] = (message.get_timestamps() & 0x00000000000000ff)448 bytes_to_send[24] = (message.get_dlc() & 0xff000000) >> 24449 bytes_to_send[25] = (message.get_dlc() & 0x00ff0000) >> 16450 bytes_to_send[26] = (message.get_dlc() & 0x0000ff00) >> 8451 bytes_to_send[27] = (message.get_dlc() & 0x000000ff)452 for x in range(28, self.global_parameter.get_global_datagram_size()):453 bytes_to_send[x] = 0454 return bytes_to_send455 def encode_handshake_message(self, message):456 bytes_to_send = bytearray(self.global_parameter.get_global_datagram_size())457 data_type_msb = message.get_message_id() // (2 ** 32)458 data_type_lsb = message.get_message_id() % (2 ** 32)459 bytes_to_send[0] = (data_type_msb & 0xff000000) >> 24460 bytes_to_send[1] = (data_type_msb & 0x00ff0000) >> 16461 bytes_to_send[2] = (data_type_msb & 0x0000ff00) >> 8462 bytes_to_send[3] = (data_type_msb & 0x000000ff)463 bytes_to_send[4] = (data_type_lsb & 0xff000000) >> 24464 bytes_to_send[5] = (data_type_lsb & 0x00ff0000) >> 16465 bytes_to_send[6] = (data_type_lsb & 0x0000ff00) >> 8466 bytes_to_send[7] = (data_type_lsb & 0x000000ff)467 bytes_to_send[8] = (message.get_target_id() & 0xff000000) >> 24468 bytes_to_send[9] = (message.get_target_id() & 0x00ff0000) >> 16469 bytes_to_send[10] = (message.get_target_id() & 0x0000ff00) >> 8470 bytes_to_send[11] = (message.get_target_id() & 0x000000ff)471 bytes_to_send[12] = (message.get_origin_id() & 0xff000000) >> 24472 bytes_to_send[13] = (message.get_origin_id() & 0x00ff0000) >> 16473 bytes_to_send[14] = (message.get_origin_id() & 0x0000ff00) >> 8474 bytes_to_send[15] = (message.get_origin_id() & 0x000000ff)475 bytes_to_send[16] = (message.get_timestamps() & 0xff00000000000000) >> 56476 bytes_to_send[17] = (message.get_timestamps() & 0x00ff000000000000) >> 48477 bytes_to_send[18] = (message.get_timestamps() & 0x0000ff0000000000) >> 40478 bytes_to_send[19] = (message.get_timestamps() & 0x000000ff00000000) >> 32479 bytes_to_send[20] = (message.get_timestamps() & 0x00000000ff000000) >> 24480 bytes_to_send[21] = (message.get_timestamps() & 0x0000000000ff0000) >> 16481 bytes_to_send[22] = (message.get_timestamps() & 0x000000000000ff00) >> 8482 bytes_to_send[23] = (message.get_timestamps() & 0x00000000000000ff)483 bytes_to_send[24] = (message.get_dlc() & 0xff000000) >> 24484 bytes_to_send[25] = (message.get_dlc() & 0x00ff0000) >> 16...
Hit.py
Source:Hit.py
...129 self.alignment = alignment130 def keys(self):131 '''Returns a list of tuples that will be used as keys for this hit in a hitlist.'''132 if self.get_seq_id is not None and self.get_target_id is not None:133 return [(self.get_seq_id(), self.get_target_id(), self.seq_location[0], self.target_location[0]),134 (self.get_seq_id(), self.get_target_id(), self.seq_location[1], self.target_location[1]),135 (self.get_seq_id(), self.get_target_id(), self.seq_location[0], self.target_location[0])]136 else:137 return None138 def _check_rc(self):139 '''140 Returns True if the current hit is a hit on the reversed complement of a141 sequence originally read from a file.142 '''143 return(self.get_seq_id()[-2:] == "RC" and self.get_target_id()[-2:] == "RC")144 def get_seq_id(self):145 '''Returns the ID of the sequence that contains the current alignment.'''146 return self.sequence_info.id147 def get_target_id(self):148 '''Returns the ID of the target that contains the current alignment.'''149 return self.target_info.id150 def get_euclidian_distance(self):151 '''Returns the calculated Euclidian distance between sequence and target'''152 if self.target_info.distance is None:153 return 0.0154 else:155 return self.target_info.distance156 def get_graph_relation(self, prefix, targetID, sequence_node, target_node):157 158 relParameters = "seq_start:{},seq_end:{},".format(self.seq_location[0], self.seq_location[1])159 relParameters += "target_start:{},target_end:{},".format(self.target_location[0], self.target_location[1])160 relParameters += "score: {}, length: {}, ".format(self.score, len(self.alignment))161 relParameters += "relative_score: {}, base_score: {}, ".format(self.relative_score, self.base_score)162 relParameters += "query_identity: {}, query_coverage: {}, ".format(self.query_identity, self.query_coverage)163 164 if targetID == self.get_target_id():165 relParameters += "direction:'forward'"166 else:167 relParameters += "direction:'reverse'"168 relation = "AlignsWith"169 170 if self.target_location[0] - self.seq_location[0] >= 0 and self.target_location[1] + (self.sequence_info.original_length - self.seq_location[1]) <= self.target_info.original_length:171 relation = "AlignsIn"172 relParameters += ",extends: 0"173 elif (self.target_location[0] - self.seq_location[0] >= 0 and self.target_location[1] + 1 == self.target_info.original_length) or (self.target_location[0] == 0 and self.target_location[1] + 1 + (self.sequence_info.original_length - self.seq_location[1]) <= self.target_info.original_length):174 relation = "Extends"175 if self.target_location[1] + 1 == self.target_info.original_length:176 relation += "End"177 relParameters += ",extends: {}".format(self.sequence_info.original_length-self.seq_location[1])178 else:179 relation += "Start"180 relParameters += ",extends: {}".format(self.seq_location[0])181 elif (self.target_location[0] - self.seq_location[0] >= 0 and self.target_location[1] + (self.sequence_info.original_length - self.seq_location[1]) > self.target_info.original_length) or (self.target_location[0] - self.seq_location[0] < 0 and self.target_location[1] + (self.sequence_info.original_length - self.seq_location[1]) <= self.target_info.original_length) :182 relation = "Overlaps"183 if self.target_location[1] + (self.sequence_info.original_length - self.seq_location[1]) > self.target_info.original_length:184 relParameters += ",extends: {}".format(self.sequence_info.original_length-self.seq_location[1])185 relation += "End"186 else:187 relation += "Start"188 relParameters += ",extends: {}".format(self.seq_location[0])189 else:190 relParameters += ",extends: 0"191 return "match (a:{}),(b:{}) where a.name = '{}_{}' and b.name= '{}_{}' and (not a.name = b.name) and not (a)-[:{}]->(b) create (a)-[r:{} {{ {} }}]->(b)".format(192 sequence_node, target_node, prefix, self.get_seq_id(), prefix, targetID, relation, relation,relParameters)193 def get_sam_line(self):194 '''Creates and returns an alignment line as described in http://samtools.sourceforge.net/SAM1.pdf195 The following mappings are used for record lines:196 QNAME: self.get_seq_id()197 FLAG: only bit 0x2 and 0x10 are set since the other values are either false or unknown198 RNAME: self.get_target_id()199 POS: hit.target_location[0] + 1 (+1 since SAM is 1 based!)200 MAPQ: set to 255 to indicate quality score is not available201 CIGAR: see _get_sam_cigar202 RNEXT: set to * (not available)203 PNEXT: set to 0 (not available)204 TLEN: set to 0 (not available)205 SEQ: self.sequence_info.sequence206 QUAL: set to * (not available)207 AS: self.score208 AD:f: computed euclidian distance between sequence and target209 RS:f: computed relative score210 '''211 rc_seq = False212 rc_target = False213 214 identifier = self.get_seq_id()215 if identifier[-2:] == 'RC':216 identifier = identifier[:-3]217 rc_seq = True218 target_id = self.get_target_id()219 if target_id[-2:] == 'RC':220 target_id = target_id[:-3]221 rc_target = True222 223 #rc = (rc_seq and not rc_target) or (not rc_seq and rc_target)224 self.rc = rc_target or rc_seq 225 226 hit_pos = str(self.target_location[0] + 1)227 sam_sequence = self.sequence_info.seq228 if self.rc:229 self.alignment = self.alignment[::-1]230 self.sequence_match = self.sequence_match[::-1]231 sam_sequence = Seq(str(self.sequence_info.seq), self.sequence_info.seq.alphabet).reverse_complement()232 hit_pos = str(self.target_info.original_length - self.target_location[1])233 if len(self.sequence_match) == 0 or len(self.target_match) == 0 or len(self.alignment) == 0:234 raise CudaException('sequence_match, target_match and alignment should be set and have lengths > 0.')235 return '\t'.join([identifier, self._get_sam_flag(), target_id,236 hit_pos, Hit._get_sam_mapq(), self._get_sam_cigar(),237 '*', str(0), str(0), str(sam_sequence), '*', self._get_sam_alignment_score(),238 self._get_sam_relative_score(),239 self._get_sam_relative_base_score(),240 self._get_sam_query_coverage(),241 self._get_sam_query_identity()])242 243 def get_trimmed_line(self):244 identifier = self.get_seq_id()245 if identifier[-2:] == 'RC':246 identifier = identifier[:-3]247 target_id = self.get_target_id()248 if target_id[-2:] == 'RC':249 target_id = target_id[:-3]250 if len(self.sequence_match) == 0 or len(self.target_match) == 0 or len(self.alignment) == 0:251 raise CudaException('sequence_match, target_match and alignment should be set and have lengths > 0.')252 return ''.join(['>', target_id, ' ', self.sequence_info.id, "\n", 253 str(self.sequence_info.seq[:self.target_location[0]] + self.sequence_info.seq[self.target_location[1]+1:])])254 def get_fasta(self):255 identifier = self.get_seq_id()256 if identifier[-2:] == 'RC':257 identifier = identifier[:-3]258 target_id = self.get_target_id()259 if target_id[-2:] == 'RC':260 target_id = target_id[:-3]261 if len(self.sequence_match) == 0 or len(self.target_match) == 0 or len(self.alignment) == 0:262 raise CudaException('sequence_match, target_match and alignment should be set and have lengths > 0.')263 return ''.join(['>', target_id, ' ', self.sequence_info.id, "\n", 264 str(self.sequence_info.seq[:self.target_location[0]] + self.sequence_info.seq[self.target_location[1]+1:])])265 def get_full_fasta(self):266 identifier = self.get_seq_id()267 return '>{}\n{}'.format(identifier, str(self.sequence_info.seq))268 def get_sam_sq(self):269 '''creates and returns the target (reference) information of the hit formatted270 as a SAM SQ-line. See http://samtools.sourceforge.net/SAM1.pdf271 '''272 return '\t'.join(['@SQ', 'SN:{0}'.format(self.get_target_id() if self.get_target_id()[-2:] != "RC" else self.get_target_id()[:-3]),273 'LN:{0}'.format(self.target_info.original_length)])274 def _get_sam_alignment_score(self):275 '''Returns the (optional) field containing the alignment score of the hit as an int.276 '''277 return ':'.join(['AS', 'i', str(int(self.score))])278 def _get_sam_flag(self):279 '''Assemble the FLAG field of a hit as described in http://samtools.sourceforge.net/SAM1.pdf.280 If the hit involves the reversed complement of a sequence, bit 16 is set.281 The other bits are set to 0, either because their value is unknown or False.282 '''283 flag = 0284 if self.get_seq_id()[-2:] == 'RC' or self.get_target_id()[-2:] == 'RC':285 flag += 16286 return str(flag)287 @staticmethod288 def _get_sam_mapq():289 '''Determine the MAPQ field as described in http://samtools.sourceforge.net/SAM1.pdf.290 At the moment a fixed value of 255 is returned, indicating that mapping quality is not available.291 '''292 return str(255)293 def _get_sam_cigar(self):294 '''Determines the CIGAR of a hit as described in http://samtools.sourceforge.net/SAM1.pdf.295 '''296 cigar_parts = []297 # add clipping information to cigar_parts298 if not self.rc:...
Formatters.py
Source:Formatters.py
...15 self.logger.debug('Initialized {0}'.format(self.name))16 def _format_hit(self, hit):17 '''This method may be overruled to enable other formats for printed results.'''18 self.logger.debug('Formatting hit {0}'.format(hit.get_seq_id()))19 formatted_hit = ', '.join([hit.get_seq_id(), hit.get_target_id(), str(hit.seq_location[0]), str(hit.seq_location[1]),20 str(hit.target_location[0]), str(hit.target_location[1]), str(hit.score), str(hit.matches),21 str(hit.mismatches), str(len(hit.alignment) - hit.matches - hit.mismatches),22 str(len(hit.alignment)), str(hit.score / len(hit.alignment)),23 str(hit.sequence_info.original_length), str(hit.target_info.original_length),24 str(hit.score / hit.sequence_info.original_length),25 str(hit.score / hit.target_info.original_length), str(hit.distance)])26 formatted_hit = '\n'.join([formatted_hit, hit.sequence_match, hit.alignment, hit.target_match])27 return formatted_hit28 def _set_name(self):29 '''Name of the formatter. Used for logging'''30 self.name = 'defaultformatter'31 def _get_hits(self):32 '''Returns ordered list of hits'''33 hits = self.hitlist.real_hits.values()34 return sorted(hits, key=lambda hit: (hit.get_seq_id(), hit.get_target_id(), hit.score))35 def print_results(self):36 '''sets, formats and prints the results to a file.'''37 self.logger.debug('printing results...')38 output = open(self.outputfile, 'w')39 for hit in self._get_hits():40 formatted_hit = self._format_hit(hit)41 output.write(formatted_hit + "\n")42 self.logger.debug('finished printing results')43class SamFormatter(DefaultFormatter):44 '''This Formatter is used to create SAM output45 See http://samtools.sourceforge.net/SAM1.pdf46 '''47 def __init__(self, logger, hitlist, outputfile):48 '''Since the header contains information about the target sequences and must be49 present before alignment lines, formatted lines are stored before printing.50 '''51 DefaultFormatter.__init__(self, logger, hitlist, outputfile)52 self.sq_lines = {}53 self.record_lines = []54 def _set_name(self):55 '''Name of the formatter. Used for logging'''56 self.name = 'SAM formatter'57 def _format_hit(self, hit):58 '''Adds a header line to self.sq_lines and an alignment line to self.record_lines.59 The following mappings are used for header lines:60 SN: hit.get_target_id()61 LN: hit.full_target.original_length62 '''63 self.logger.debug('Formatting hit {0}'.format(hit.get_seq_id()))64 #add a header line for the target id if not already present65 if hit.get_target_id() not in self.sq_lines:66 if hit.get_target_id()[-2:] != 'RC':67 self.sq_lines[hit.get_target_id()] = hit.get_sam_sq()68 else:69 self.sq_lines[hit.get_target_id()[:-3]] = hit.get_sam_sq()70 71 #add a line for the hit72 self.record_lines.append(hit.get_sam_line())73 def print_results(self):74 '''sets, formats and prints the results to a file.'''75 self.logger.info('formatting results...')76 #format header and hit lines77 for hit in self._get_hits():78 self._format_hit(hit)79 self.logger.debug('printing results...')80 output = open(self.outputfile, 'w')81 #write the header lines to the file82 header_string = '@HD\tVN:1.4\tSO:unknown'83 output.write(header_string + '\n')84 for header_line in self.sq_lines:85 output.write(self.sq_lines[header_line] + '\n')86 #program information header line87 output.write('@PG\tID:0\tPN:paswas\tVN:3.0\n')88 #write the hit lines to the output file89 for line in self.record_lines:90 output.write(line + '\n')91 output.close()92 self.logger.debug('finished printing results')93class TrimmerFormatter(DefaultFormatter):94 '''This Formatter is used to create SAM output95 See http://samtools.sourceforge.net/SAM1.pdf96 '''97 def __init__(self, logger, hitlist, outputfile):98 '''Since the header contains information about the target sequences and must be99 present before alignment lines, formatted lines are stored before printing.100 '''101 DefaultFormatter.__init__(self, logger, hitlist, outputfile)102 self.sq_lines = {}103 self.record_lines = []104 def _set_name(self):105 '''Name of the formatter. Used for logging'''106 self.name = 'SAM formatter'107 def _format_hit(self, hit):108 '''Adds a header line to self.sq_lines and an alignment line to self.record_lines.109 The following mappings are used for header lines:110 SN: hit.get_target_id()111 LN: hit.full_target.original_length112 '''113 self.logger.debug('Formatting hit {0}'.format(hit.get_seq_id()))114 self.record_lines.append(hit.get_trimmed_line())115 def print_results(self):116 '''sets, formats and prints the results to a file.'''117 self.logger.info('formatting results...')118 #format header and hit lines119 for hit in self._get_hits():120 self._format_hit(hit)121 self.logger.debug('printing results...')122 output = open(self.outputfile, 'w')123 #write the hit lines to the output file124 for line in self.record_lines:125 output.write(line + '\n')126 output.close()127 self.logger.debug('finished printing results')128class FASTA(DefaultFormatter):129 '''This Formatter is used to create FASTA output130 '''131 def __init__(self, logger, hitlist, outputfile):132 '''Since the header contains information about the target sequences and must be133 present before alignment lines, formatted lines are stored before printing.134 '''135 DefaultFormatter.__init__(self, logger, hitlist, outputfile)136 self.sq_lines = {}137 self.record_lines = []138 def _set_name(self):139 '''Name of the formatter. Used for logging'''140 self.name = 'FASTA formatter'141 def _format_hit(self, hit):142 '''Adds a header line to self.sq_lines and an alignment line to self.record_lines.143 The following mappings are used for header lines:144 SN: hit.get_target_id()145 LN: hit.full_target.original_length146 '''147 self.logger.debug('Formatting hit {0}'.format(hit.get_seq_id()))148 self.record_lines.append(hit.get_full_fasta())149 def print_results(self):150 '''sets, formats and prints the results to a file.'''151 self.logger.info('formatting results...')152 #format header and hit lines153 for hit in self._get_hits():154 self._format_hit(hit)155 self.logger.debug('printing results...')156 output = open(self.outputfile, 'w')157 #write the hit lines to the output file158 for line in self.record_lines:...
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