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120 additions
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1558 deletions
| ... | @@ -8,6 +8,9 @@ FEATURE CHANGES | ... | @@ -8,6 +8,9 @@ FEATURE CHANGES |
| 8 | The LSU and SSU are now aligned with Infernal options '--cpu 10 --mxsize 8192 --mxtau 0.1', which is slow, | 8 | The LSU and SSU are now aligned with Infernal options '--cpu 10 --mxsize 8192 --mxtau 0.1', which is slow, |
| 9 | requires up to 100 GB of RAM, and yields a suboptimal alignment (tau=0.1 is quite bad), but is homogenous with the other families. | 9 | requires up to 100 GB of RAM, and yields a suboptimal alignment (tau=0.1 is quite bad), but is homogenous with the other families. |
| 10 | - The LSU and SSU therefore have defined cm_coords fields, and therefore distance matrices can be computed. | 10 | - The LSU and SSU therefore have defined cm_coords fields, and therefore distance matrices can be computed. |
| 11 | + - Distances matrices are computed on all availables molecules of the family by default, but you can use statistics.py --non-redundant to only | ||
| 12 | + select the equivalence class representatives at a given resolution into account (new option). For storage reasons, rRNAs are always run in | ||
| 13 | + this mode (but this might change in the future : space required is 'only' ~300 GB). | ||
| 11 | - We now provide for download the renumbered (standardised) 3D MMCIF files, the nucleotides being numbered by their "index_chain" in the database. | 14 | - We now provide for download the renumbered (standardised) 3D MMCIF files, the nucleotides being numbered by their "index_chain" in the database. |
| 12 | - We now provide for download the sequences of the 3D chains aligned by Rfam family (without Rfam sequences, which have been removed). | 15 | - We now provide for download the sequences of the 3D chains aligned by Rfam family (without Rfam sequences, which have been removed). |
| 13 | - statistics.py now computes histograms and a density estimation with Gaussian mixture models for a large set of geometric parameters, | 16 | - statistics.py now computes histograms and a density estimation with Gaussian mixture models for a large set of geometric parameters, |
| ... | @@ -23,7 +26,7 @@ FEATURE CHANGES | ... | @@ -23,7 +26,7 @@ FEATURE CHANGES |
| 23 | BUG CORRECTIONS | 26 | BUG CORRECTIONS |
| 24 | - New code file geometric_stats.py | 27 | - New code file geometric_stats.py |
| 25 | - New automation script that starts from scratch | 28 | - New automation script that starts from scratch |
| 26 | - - Many small fixes | 29 | + - Many small fixes, leading to the support of many previously "known issues" |
| 27 | - Performance tweaks | 30 | - Performance tweaks |
| 28 | 31 | ||
| 29 | TECHNICAL CHANGES | 32 | TECHNICAL CHANGES | ... | ... |
| 1 | -6cfj_1_1X | ||
| 2 | -6cfj_1_2X | ||
| 3 | -5hcq_1_1X | ||
| 4 | -6cae_1_1X | ||
| 5 | -5hcq_1_2X | ||
| 6 | -5hcr_1_1X | ||
| 7 | -4z8c_1_1X | ||
| 8 | -5j4b_1_1X | ||
| 9 | -6xhy_1_1X | ||
| 10 | -6xhy_1_2X | ||
| 11 | -5j4b_1_2X | ||
| 12 | -4z8c_1_2X | ||
| 13 | -6cae_1_2X | ||
| 14 | -5j4c_1_1X | ||
| 15 | -5w4k_1_1X | ||
| 16 | -6of1_1_1X | ||
| 17 | -6xhw_1_1X | ||
| 18 | -5hcr_1_2X | ||
| 19 | -5hd1_1_1X | ||
| 20 | -5hcp_1_1X | ||
| 21 | -6of1_1_2X | ||
| 22 | -5hau_1_1W | ||
| 23 | -5j4c_1_2X | ||
| 24 | -5wis_1_1X | ||
| 25 | -6xhv_1_1X | ||
| 26 | -6xqd_1_1X | ||
| 27 | -6nd5_1_1X | ||
| 28 | -5w4k_1_2X | ||
| 29 | -6xhw_1_2X | ||
| 30 | -5hau_1_2W | ||
| 31 | -6xqd_1_2X | ||
| 32 | -6xhv_1_2X | ||
| 33 | -4y4p_1_1X | ||
| 34 | -6o97_1_1X | ||
| 35 | -5hcp_1_2X | ||
| 36 | -5doy_1_1X | ||
| 37 | -4zer_1_1X | ||
| 38 | -5wit_1_1X | ||
| 39 | -5hd1_1_2X | ||
| 40 | -6nd5_1_2X | ||
| 41 | -4z3s_1_1X | ||
| 42 | -7jql_1_1X | ||
| 43 | -7jqm_1_1X | ||
| 44 | -7jql_1_2X | ||
| 45 | -5wis_1_2X | ||
| 46 | -6nd6_1_1X | ||
| 47 | -6o97_1_2X | ||
| 48 | -4y4p_1_2X | ||
| 49 | -7jqm_1_2X | ||
| 50 | -4z3s_1_2X | ||
| 51 | -4zer_1_2X | ||
| 52 | -6uo1_1_2X | ||
| 53 | -6uo1_1_1X | ||
| 54 | -5doy_1_2X | ||
| 55 | -5wit_1_2X | ||
| 56 | -5f8k_1_1X | ||
| 57 | -6nd6_1_2X | ||
| 58 | -6xqe_1_1X | ||
| 59 | -6xqe_1_2X | ||
| 60 | -6n9e_1_1X | ||
| 61 | -6n9e_1_2X | ||
| 62 | -6n9f_1_1X | ||
| 63 | -5f8k_1_2X | ||
| 64 | -6n9f_1_2X | ||
| 65 | -6xz7_1_F | ||
| 66 | -6xzb_1_F2 | ||
| 67 | -6xza_1_F2 | ||
| 68 | -6y69_1_W | ||
| 69 | -5afi_1_V | ||
| 70 | -5afi_1_W | ||
| 71 | -6h4n_1_W | ||
| 72 | -5wdt_1_V | ||
| 73 | -5wfs_1_V | ||
| 74 | -5wdt_1_W | ||
| 75 | -5wfs_1_W | ||
| 76 | -5we4_1_V | ||
| 77 | -5we4_1_W | ||
| 78 | -5uq8_1_Y | ||
| 79 | -6c4i_1_Y | ||
| 80 | -6c4i_1_X | ||
| 81 | -6yef_1_X | ||
| 82 | -5zeb_1_V | ||
| 83 | -5zep_1_W | ||
| 84 | -5lzd_1_V | ||
| 85 | -5we6_1_V | ||
| 86 | -5wfk_1_V | ||
| 87 | -5wfk_1_W | ||
| 88 | -5we6_1_W | ||
| 89 | -5u4i_1_Y | ||
| 90 | -5uq7_1_Y | ||
| 91 | -5u4i_1_X | ||
| 92 | -5lza_1_V | ||
| 93 | -5wf0_1_V | ||
| 94 | -5wf0_1_W | ||
| 95 | -5zeu_1_V | ||
| 96 | -5l3p_1_X | ||
| 97 | -3jcj_1_V | ||
| 98 | -6gxm_1_X | ||
| 99 | -6gwt_1_X | ||
| 100 | -6gxn_1_X | ||
| 101 | -6gxo_1_X | ||
| 102 | -3j9y_1_V | ||
| 103 | -6o9k_1_Y | ||
| 104 | -6o7k_1_V | ||
| 105 | -5lzf_1_V | ||
| 106 | -3jcn_1_V | ||
| 107 | -5lzc_1_V | ||
| 108 | -5u4j_1_X | ||
| 109 | -5u4j_1_Z | ||
| 110 | -5lzb_1_V | ||
| 111 | -6h58_1_W | ||
| 112 | -6h58_1_WW | ||
| 113 | -5j8b_1_X | ||
| 114 | -4v7j_1_AV | ||
| 115 | -4v7j_1_BV | ||
| 116 | -4v7k_1_BV | ||
| 117 | -4v7k_1_AV | ||
| 118 | -4v7k_1_BW | ||
| 119 | -4v7k_1_AW | ||
| 120 | -4v7j_1_AW | ||
| 121 | -4v7j_1_BW | ||
| 122 | -4v4j_1_Z | ||
| 123 | -6i0v_1_B | ||
| 124 | -5k77_1_X | ||
| 125 | -5k77_1_V | ||
| 126 | -5k77_1_Y | ||
| 127 | -5k77_1_W | ||
| 128 | -5k77_1_Z | ||
| 129 | -4pei_1_X | ||
| 130 | -4pei_1_V | ||
| 131 | -4pei_1_W | ||
| 132 | -4pei_1_Z | ||
| 133 | -4pei_1_Y | ||
| 134 | -4a3c_1_P | ||
| 135 | -4a3e_1_P | ||
| 136 | -6lkq_1_U | ||
| 137 | -7k00_1_B | ||
| 138 | -6ys3_1_A | ||
| 139 | -6qdw_1_A | ||
| 140 | -6hcj_1_Q3 | ||
| 141 | -6hcq_1_Q3 | ||
| 142 | -6o8w_1_U | ||
| 143 | -5mmm_1_Z | ||
| 144 | -4w2e_1_W | ||
| 145 | -5j4b_1_1Y | ||
| 146 | -6cfj_1_1W | ||
| 147 | -5w4k_1_1Y | ||
| 148 | -6xhy_1_1W | ||
| 149 | -5wit_1_1W | ||
| 150 | -6cfj_1_1Y | ||
| 151 | -6cfj_1_2W | ||
| 152 | -5j4c_1_1W | ||
| 153 | -5wis_1_1Y | ||
| 154 | -5j4c_1_1Y | ||
| 155 | -6xhw_1_1W | ||
| 156 | -6cfj_1_2Y | ||
| 157 | -5wis_1_1W | ||
| 158 | -5j4b_1_1W | ||
| 159 | -6xhv_1_1W | ||
| 160 | -6xhy_1_2W | ||
| 161 | -5j4c_1_2W | ||
| 162 | -5j4b_1_2W | ||
| 163 | -5j4b_1_2Y | ||
| 164 | -5j4c_1_2Y | ||
| 165 | -5w4k_1_1W | ||
| 166 | -6nd5_1_1Y | ||
| 167 | -6xhw_1_2W | ||
| 168 | -5wis_1_2Y | ||
| 169 | -5wit_1_2W | ||
| 170 | -6xhv_1_2W | ||
| 171 | -5doy_1_1Y | ||
| 172 | -5w4k_1_2Y | ||
| 173 | -4y4p_1_1Y | ||
| 174 | -4z3s_1_1Y | ||
| 175 | -5doy_1_1W | ||
| 176 | -5doy_1_2Y | ||
| 177 | -6nd5_1_1W | ||
| 178 | -4z3s_1_2Y | ||
| 179 | -4z3s_1_1W | ||
| 180 | -5w4k_1_2W | ||
| 181 | -6nd5_1_2Y | ||
| 182 | -4y4p_1_2Y | ||
| 183 | -6uo1_1_2Y | ||
| 184 | -6uo1_1_2W | ||
| 185 | -4y4p_1_1W | ||
| 186 | -4z3s_1_2W | ||
| 187 | -6uo1_1_1Y | ||
| 188 | -6xhy_1_1Y | ||
| 189 | -6uo1_1_1W | ||
| 190 | -5wis_1_2W | ||
| 191 | -5wit_1_1Y | ||
| 192 | -6nd5_1_2W | ||
| 193 | -4y4p_1_2W | ||
| 194 | -5doy_1_2W | ||
| 195 | -5wit_1_2Y | ||
| 196 | -6xhv_1_1Y | ||
| 197 | -6xhy_1_2Y | ||
| 198 | -6xhw_1_1Y | ||
| 199 | -6xhw_1_2Y | ||
| 200 | -6ucq_1_1Y | ||
| 201 | -6xhv_1_2Y | ||
| 202 | -4v4i_1_Z | ||
| 203 | -6ucq_1_1X | ||
| 204 | -6ucq_1_2Y | ||
| 205 | -4w2e_1_X | ||
| 206 | -6ucq_1_2X | ||
| 207 | -7n1p_1_DT | ||
| 208 | -7n2u_1_DT | ||
| 209 | -6yss_1_W | ||
| 210 | -7n30_1_DT | ||
| 211 | -7n31_1_DT | ||
| 212 | -7n2c_1_DT | ||
| 213 | -5afi_1_Y | ||
| 214 | -5uq8_1_Z | ||
| 215 | -5wdt_1_Y | ||
| 216 | -5wfs_1_Y | ||
| 217 | -6ysr_1_W | ||
| 218 | -5we4_1_Y | ||
| 219 | -6yst_1_W | ||
| 220 | -5uq7_1_Z | ||
| 221 | -5we6_1_Y | ||
| 222 | -5wfk_1_Y | ||
| 223 | -5wf0_1_Y | ||
| 224 | -6o9j_1_V | ||
| 225 | -6ysu_1_W | ||
| 226 | -3j46_1_A | ||
| 227 | -5j8b_1_Y | ||
| 228 | -5j8b_1_W | ||
| 229 | -3bbv_1_Z | ||
| 230 | -5aj0_1_BV | ||
| 231 | -5aj0_1_BW | ||
| 232 | -4wt8_1_AB | ||
| 233 | -4wt8_1_BB | ||
| 234 | -4v4j_1_Y | ||
| 235 | -4v4i_1_Y | ||
| 236 | -5uq8_1_X | ||
| 237 | -5uq7_1_X | ||
| 238 | -4v4j_1_W | ||
| 239 | -4v4i_1_W | ||
| 240 | -4wt8_1_CS | ||
| 241 | -4wt8_1_DS | ||
| 242 | -4v4j_1_X | ||
| 243 | -4v4i_1_X | ||
| 244 | -6lkq_1_S | ||
| 245 | -5h5u_1_H | ||
| 246 | -7d6z_1_F | ||
| 247 | -5lze_1_Y | ||
| 248 | -5lze_1_V | ||
| 249 | -5lze_1_X | ||
| 250 | -3jcj_1_G | ||
| 251 | -6o7k_1_G | ||
| 252 | -6d30_1_C | ||
| 253 | -6j7z_1_C | ||
| 254 | -3er9_1_D | ||
| 255 | -5kal_1_Y | ||
| 256 | -4nia_1_3 | ||
| 257 | -5kal_1_Z | ||
| 258 | -4nia_1_7 | ||
| 259 | -4nia_1_4 | ||
| 260 | -5new_1_C | ||
| 261 | -4nia_1_U | ||
| 262 | -4nia_1_6 | ||
| 263 | -4oq9_1_7 | ||
| 264 | -4nia_1_1 | ||
| 265 | -4oq9_1_4 | ||
| 266 | -4nia_1_8 | ||
| 267 | -4oq9_1_8 | ||
| 268 | -4nia_1_5 | ||
| 269 | -2vrt_1_E | ||
| 270 | -4nia_1_W | ||
| 271 | -4oq9_1_6 | ||
| 272 | -4oq8_1_D | ||
| 273 | -4nia_1_Z | ||
| 274 | -4oq9_1_W | ||
| 275 | -4oq9_1_5 | ||
| 276 | -4nia_1_2 | ||
| 277 | -2vrt_1_F | ||
| 278 | -4oq9_1_U | ||
| 279 | -4oq9_1_Z | ||
| 280 | -4oq9_1_2 | ||
| 281 | -4oq9_1_3 | ||
| 282 | -1ddl_1_E | ||
| 283 | -4oq9_1_1 | ||
| 284 | -6rt5_1_A | ||
| 285 | -6rt5_1_E | ||
| 286 | -6lkq_1_T | ||
| 287 | -6ys3_1_B | ||
| 288 | -6qdw_1_B | ||
| 289 | -3jbv_1_B | ||
| 290 | -3jbu_1_B | ||
| 291 | -6do8_1_B | ||
| 292 | -6dpi_1_B | ||
| 293 | -6dp9_1_B | ||
| 294 | -6dpb_1_B | ||
| 295 | -6dmn_1_B | ||
| 296 | -6dpp_1_B | ||
| 297 | -6dpk_1_B | ||
| 298 | -6dpd_1_B | ||
| 299 | -6dot_1_B | ||
| 300 | -6dok_1_B | ||
| 301 | -6dp8_1_B | ||
| 302 | -6dpl_1_B | ||
| 303 | -6dpg_1_B | ||
| 304 | -6dou_1_B | ||
| 305 | -6dpc_1_B | ||
| 306 | -6do9_1_B | ||
| 307 | -6dmv_1_B | ||
| 308 | -6dp4_1_B | ||
| 309 | -6dpn_1_B | ||
| 310 | -6doj_1_B | ||
| 311 | -6dph_1_B | ||
| 312 | -6dos_1_B | ||
| 313 | -6doo_1_B | ||
| 314 | -6dp6_1_B | ||
| 315 | -6dox_1_B | ||
| 316 | -6dp5_1_B | ||
| 317 | -6dol_1_B | ||
| 318 | -6dp1_1_B | ||
| 319 | -6doz_1_B | ||
| 320 | -6dp7_1_B | ||
| 321 | -6doq_1_B | ||
| 322 | -6dpa_1_B | ||
| 323 | -6dom_1_B | ||
| 324 | -6dog_1_B | ||
| 325 | -6dop_1_B | ||
| 326 | -6doh_1_B | ||
| 327 | -6doa_1_B | ||
| 328 | -6don_1_B | ||
| 329 | -6dov_1_B | ||
| 330 | -6dpo_1_B | ||
| 331 | -6dod_1_B | ||
| 332 | -6dob_1_B | ||
| 333 | -6dow_1_B | ||
| 334 | -6dpm_1_B | ||
| 335 | -6dpf_1_B | ||
| 336 | -6dp3_1_B | ||
| 337 | -6dp2_1_B | ||
| 338 | -6dpe_1_B | ||
| 339 | -6dpj_1_B | ||
| 340 | -6dor_1_B | ||
| 341 | -6dof_1_B | ||
| 342 | -6dp0_1_B | ||
| 343 | -6doi_1_B | ||
| 344 | -6doc_1_B | ||
| 345 | -6doe_1_B | ||
| 346 | -6n6g_1_D | ||
| 347 | -4b3r_1_W | ||
| 348 | -4b3t_1_W | ||
| 349 | -4b3s_1_W | ||
| 350 | -7b5k_1_X | ||
| 351 | -5o2r_1_X | ||
| 352 | -5kcs_1_1X | ||
| 353 | -7n1p_1_PT | ||
| 354 | -7n2u_1_PT | ||
| 355 | -7n30_1_PT | ||
| 356 | -7n31_1_PT | ||
| 357 | -7n2c_1_PT | ||
| 358 | -6zvk_1_E2 | ||
| 359 | -6zvk_1_H2 | ||
| 360 | -7a01_1_E2 | ||
| 361 | -7a01_1_H2 | ||
| 362 | -6fti_1_U | ||
| 363 | -6fti_1_W | ||
| 364 | -6ftj_1_U | ||
| 365 | -6ftj_1_W | ||
| 366 | -6ftg_1_U | ||
| 367 | -6ftg_1_W | ||
| 368 | -6x1b_1_D | ||
| 369 | -6x1b_1_F | ||
| 370 | -5f6c_1_C | ||
| 371 | -6i0t_1_B | ||
| 372 | -1b2m_1_C | ||
| 373 | -1b2m_1_D | ||
| 374 | -1b2m_1_E | ||
| 375 | -2uxc_1_Y | ||
| 376 | -4a3g_1_P | ||
| 377 | -4a3j_1_P | ||
| 378 | -7k00_1_5 | ||
| 379 | -5mmi_1_Z | ||
| 380 | -3j9m_1_U | ||
| 381 | -7a5k_1_U3 | ||
| 382 | -6nu2_1_U | ||
| 383 | -7a5g_1_U3 | ||
| 384 | -6nu3_1_U | ||
| 385 | -5c0y_1_C | ||
| 386 | -6n6f_1_D | ||
| 387 | -4ohy_1_B | ||
| 388 | -4oi1_1_B | ||
| 389 | -4oi0_1_B | ||
| 390 | -5ipl_1_3 | ||
| 391 | -6utw_1_333 | ||
| 392 | -5ipm_1_3 | ||
| 393 | -5ipn_1_3 | ||
| 394 | -4ylo_1_3 | ||
| 395 | -4yln_1_6 | ||
| 396 | -4ylo_1_6 | ||
| 397 | -4yln_1_3 | ||
| 398 | -4yln_1_9 | ||
| 399 | -5lzf_1_Y | ||
| 400 | -1n32_1_Z | ||
| 401 | -5zsl_1_D | ||
| 402 | -5zsd_1_C | ||
| 403 | -5zsd_1_D | ||
| 404 | -5zsl_1_E | ||
| 405 | -4nku_1_D | ||
| 406 | -4nku_1_H | ||
| 407 | -1cwp_1_E | ||
| 408 | -6thn_1_A | ||
| 409 | -6qik_1_Y | ||
| 410 | -6rzz_1_Y | ||
| 411 | -6ri5_1_Y | ||
| 412 | -6qt0_1_Y | ||
| 413 | -6qtz_1_Y | ||
| 414 | -6t83_1_1B | ||
| 415 | -6t83_1_3B | ||
| 416 | -6t83_1_AA | ||
| 417 | -6t83_1_CA | ||
| 418 | -6s05_1_Y | ||
| 419 | -5jcs_1_X | ||
| 420 | -5fl8_1_X | ||
| 421 | -6ole_1_V | ||
| 422 | -6om0_1_V | ||
| 423 | -6oli_1_V | ||
| 424 | -6om7_1_V | ||
| 425 | -6w6l_1_V | ||
| 426 | -6olf_1_V | ||
| 427 | -3erc_1_G | ||
| 428 | -6of1_1_1W | ||
| 429 | -6cae_1_1Y | ||
| 430 | -6o97_1_1W | ||
| 431 | -6of1_1_1Y | ||
| 432 | -6of1_1_2W | ||
| 433 | -6o97_1_1Y | ||
| 434 | -6nd6_1_1Y | ||
| 435 | -6cae_1_1W | ||
| 436 | -6of1_1_2Y | ||
| 437 | -6cae_1_2Y | ||
| 438 | -6nd6_1_1W | ||
| 439 | -6cae_1_2W | ||
| 440 | -6o97_1_2Y | ||
| 441 | -6nd6_1_2Y | ||
| 442 | -6o97_1_2W | ||
| 443 | -6nd6_1_2W | ||
| 444 | -4wtm_1_T | ||
| 445 | -4wtm_1_P | ||
| 446 | -6gz4_1_BW | ||
| 447 | -6xz7_1_G | ||
| 448 | -6xzb_1_G2 | ||
| 449 | -6gz5_1_BW | ||
| 450 | -6gz3_1_BW | ||
| 451 | -4hot_1_X | ||
| 452 | -6d2z_1_C | ||
| 453 | -7eh0_1_I | ||
| 454 | -4tu0_1_F | ||
| 455 | -4tu0_1_G | ||
| 456 | -6r9o_1_B | ||
| 457 | -6is0_1_C | ||
| 458 | -5lzc_1_X | ||
| 459 | -5lzb_1_X | ||
| 460 | -5lzd_1_Y | ||
| 461 | -5lzc_1_Y | ||
| 462 | -5lzb_1_Y | ||
| 463 | -6zvi_1_E | ||
| 464 | -6sv4_1_MC | ||
| 465 | -6sv4_1_MB | ||
| 466 | -7nrd_1_SM | ||
| 467 | -6i7o_1_MB | ||
| 468 | -6zvi_1_D | ||
| 469 | -6sv4_1_NB | ||
| 470 | -6sv4_1_NC | ||
| 471 | -6i7o_1_NB | ||
| 472 | -7nsq_1_V | ||
| 473 | -6swa_1_Q | ||
| 474 | -6swa_1_R | ||
| 475 | -6ole_1_T | ||
| 476 | -6om0_1_T | ||
| 477 | -6oli_1_T | ||
| 478 | -6om7_1_T | ||
| 479 | -6olf_1_T | ||
| 480 | -6w6l_1_T | ||
| 481 | -6tnu_1_M | ||
| 482 | -5mc6_1_M | ||
| 483 | -7nrc_1_SM | ||
| 484 | -6tb3_1_N | ||
| 485 | -7b7d_1_SM | ||
| 486 | -7b7d_1_SN | ||
| 487 | -6tnu_1_N | ||
| 488 | -7nrc_1_SN | ||
| 489 | -7nrd_1_SN | ||
| 490 | -6zot_1_C | ||
| 491 | -4qu6_1_B | ||
| 492 | -2uxb_1_X | ||
| 493 | -2x1f_1_B | ||
| 494 | -2x1a_1_B | ||
| 495 | -5o1y_1_B | ||
| 496 | -4kzy_1_I | ||
| 497 | -4kzz_1_I | ||
| 498 | -4kzx_1_I | ||
| 499 | -6dzi_1_H | ||
| 500 | -5zeu_1_A | ||
| 501 | -6evj_1_N | ||
| 502 | -6evj_1_M | ||
| 503 | -6wub_1_A | ||
| 504 | -6wua_1_A | ||
| 505 | -6mpi_1_W | ||
| 506 | -5mfx_1_B | ||
| 507 | -5w0m_1_J | ||
| 508 | -5bud_1_E | ||
| 509 | -5w0m_1_I | ||
| 510 | -5w0m_1_H | ||
| 511 | -4j7m_1_B | ||
| 512 | -5bud_1_D | ||
| 513 | -6a4e_1_B | ||
| 514 | -6a4e_1_D | ||
| 515 | -6hxx_1_AA | ||
| 516 | -6hxx_1_AB | ||
| 517 | -6hxx_1_AC | ||
| 518 | -6hxx_1_AD | ||
| 519 | -6hxx_1_AE | ||
| 520 | -6hxx_1_AF | ||
| 521 | -6hxx_1_AG | ||
| 522 | -6hxx_1_AH | ||
| 523 | -6hxx_1_AI | ||
| 524 | -6hxx_1_AJ | ||
| 525 | -6hxx_1_AK | ||
| 526 | -6hxx_1_AL | ||
| 527 | -6hxx_1_AM | ||
| 528 | -6hxx_1_AN | ||
| 529 | -6hxx_1_AO | ||
| 530 | -6hxx_1_AP | ||
| 531 | -6hxx_1_AQ | ||
| 532 | -6hxx_1_AR | ||
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| 534 | -6hxx_1_AT | ||
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| 536 | -6hxx_1_AV | ||
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| 538 | -6hxx_1_AX | ||
| 539 | -6hxx_1_AY | ||
| 540 | -6hxx_1_AZ | ||
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| 543 | -6hxx_1_BC | ||
| 544 | -6hxx_1_BD | ||
| 545 | -6hxx_1_BE | ||
| 546 | -6hxx_1_BF | ||
| 547 | -6hxx_1_BG | ||
| 548 | -6hxx_1_BH | ||
| 549 | -6hxx_1_BI | ||
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| 552 | -5odv_1_C | ||
| 553 | -5odv_1_D | ||
| 554 | -5odv_1_E | ||
| 555 | -5odv_1_F | ||
| 556 | -5odv_1_G | ||
| 557 | -5odv_1_H | ||
| 558 | -5odv_1_I | ||
| 559 | -5odv_1_J | ||
| 560 | -5odv_1_K | ||
| 561 | -5odv_1_L | ||
| 562 | -5odv_1_M | ||
| 563 | -5odv_1_N | ||
| 564 | -5odv_1_O | ||
| 565 | -5odv_1_P | ||
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| 567 | -5odv_1_R | ||
| 568 | -5odv_1_S | ||
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| 570 | -5odv_1_U | ||
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| 573 | -5odv_1_X | ||
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| 593 | -6ip8_1_ZY | ||
| 594 | -6ip5_1_ZY | ||
| 595 | -6ip5_1_ZU | ||
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| 624 | -3jb7_1_M | ||
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| 658 | -6q1h_1_D | ||
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| 666 | -6wan_1_H | ||
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| 826 | -4xlr_1_T | ||
| 827 | -4xln_1_Q | ||
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| 829 | -5i2d_1_V | ||
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| 831 | -6sty_1_C | ||
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| 836 | -3ok4_1_Z | ||
| 837 | -3ok4_1_4 | ||
| 838 | -3ok4_1_V | ||
| 839 | -3ok4_1_X | ||
| 840 | -3ok4_1_P | ||
| 841 | -3ok4_1_H | ||
| 842 | -3ok4_1_J | ||
| 843 | -3ok4_1_R | ||
| 844 | -3ok4_1_T | ||
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| 883 | -6gz4_1_BV | ||
| 884 | -6gz3_1_BV | ||
| 885 | -6fti_1_Q | ||
| 886 | -7njc_1_B | ||
| 887 | -4v7e_1_AB | ||
| 888 | -4v7e_1_AE | ||
| 889 | -4v7e_1_AD | ||
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| 891 | -4x64_1_B | ||
| 892 | -4x65_1_B | ||
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| 894 | -4x66_1_B | ||
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| 908 | -4csf_1_C | ||
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| 911 | -4csf_1_E | ||
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| 921 | -2xpj_1_D | ||
| 922 | -2vrt_1_H | ||
| 923 | -2vrt_1_G | ||
| 924 | -6r9m_1_B | ||
| 925 | -4nia_1_C | ||
| 926 | -4nia_1_A | ||
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| 928 | -4nia_1_N | ||
| 929 | -4nia_1_G | ||
| 930 | -4nia_1_D | ||
| 931 | -4nia_1_B | ||
| 932 | -4nia_1_I | ||
| 933 | -4nia_1_E | ||
| 934 | -4nia_1_M | ||
| 935 | -4oq9_1_I | ||
| 936 | -4oq9_1_G | ||
| 937 | -4oq9_1_C | ||
| 938 | -4oq9_1_H | ||
| 939 | -4oq9_1_N | ||
| 940 | -4oq9_1_A | ||
| 941 | -4oq9_1_D | ||
| 942 | -4oq9_1_E | ||
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| 944 | -4oq9_1_B | ||
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| 950 | -4wtk_1_P | ||
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| 955 | -6k32_1_T | ||
| 956 | -6k32_1_P | ||
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| 960 | -6ywe_1_AA | ||
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| 965 | -1cwp_1_D | ||
| 966 | -1cwp_1_F | ||
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| 975 | -6e4p_1_K | ||
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| 980 | -3ie1_1_G | ||
| 981 | -3s4g_1_C | ||
| 982 | -3s4g_1_B | ||
| 983 | -2qqp_1_R | ||
| 984 | -1nb7_1_E | ||
| 985 | -1nb7_1_F | ||
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| 987 | -3p6y_1_T | ||
| 988 | -3p6y_1_V | ||
| 989 | -3p6y_1_U | ||
| 990 | -3p6y_1_Q | ||
| 991 | -3p6y_1_W | ||
| 992 | -5dto_1_B | ||
| 993 | -4cxh_1_X | ||
| 994 | -1uvj_1_F | ||
| 995 | -1uvj_1_D | ||
| 996 | -1uvj_1_E | ||
| 997 | -6kqd_1_I | ||
| 998 | -6kqd_1_S | ||
| 999 | -5uh5_1_I | ||
| 1000 | -1ytu_1_F | ||
| 1001 | -1ytu_1_D | ||
| 1002 | -4kzz_1_J | ||
| 1003 | -7a09_1_F | ||
| 1004 | -5t2c_1_AN | ||
| 1005 | -3j6b_1_E | ||
| 1006 | -4v4f_1_B6 | ||
| 1007 | -4v4f_1_A5 | ||
| 1008 | -4v4f_1_A3 | ||
| 1009 | -4v4f_1_B0 | ||
| 1010 | -4v4f_1_B9 | ||
| 1011 | -4v4f_1_A2 | ||
| 1012 | -4v4f_1_A8 | ||
| 1013 | -4v4f_1_A1 | ||
| 1014 | -4v4f_1_A9 | ||
| 1015 | -4v4f_1_BZ | ||
| 1016 | -4v4f_1_B8 | ||
| 1017 | -4v4f_1_B7 | ||
| 1018 | -4v4f_1_B5 | ||
| 1019 | -4v4f_1_A0 | ||
| 1020 | -4v4f_1_A7 | ||
| 1021 | -4v4f_1_A4 | ||
| 1022 | -4v4f_1_AZ | ||
| 1023 | -4v4f_1_B3 | ||
| 1024 | -4v4f_1_B1 | ||
| 1025 | -4v4f_1_B4 | ||
| 1026 | -4v4f_1_A6 | ||
| 1027 | -4v4f_1_B2 | ||
| 1028 | -7m4y_1_V | ||
| 1029 | -7m4x_1_V | ||
| 1030 | -6v3a_1_V | ||
| 1031 | -6v39_1_V | ||
| 1032 | -5it9_1_I | ||
| 1033 | -7jqc_1_I | ||
| 1034 | -5zsb_1_C | ||
| 1035 | -5zsb_1_D | ||
| 1036 | -5zsn_1_D | ||
| 1037 | -5zsn_1_E | ||
| 1038 | -6gfw_1_R | ||
| 1039 | -6zm6_1_X | ||
| 1040 | -6zm5_1_X | ||
| 1041 | -6zm6_1_W | ||
| 1042 | -6zm5_1_W | ||
| 1043 | -6n6e_1_D | ||
| 1044 | -4g7o_1_I | ||
| 1045 | -4g7o_1_S | ||
| 1046 | -5x22_1_S | ||
| 1047 | -5x22_1_I | ||
| 1048 | -5x21_1_I | ||
| 1049 | -5uh6_1_I | ||
| 1050 | -6l74_1_I | ||
| 1051 | -5uh9_1_I | ||
| 1052 | -7a5j_1_X | ||
| 1053 | -6sag_1_R | ||
| 1054 | -4udv_1_R | ||
| 1055 | -5zsc_1_D | ||
| 1056 | -5zsc_1_C | ||
| 1057 | -6woy_1_I | ||
| 1058 | -6wox_1_I | ||
| 1059 | -4gkk_1_W | ||
| 1060 | -4v9e_1_AG | ||
| 1061 | -4v9e_1_BM | ||
| 1062 | -4v9e_1_AM | ||
| 1063 | -4v9e_1_AA | ||
| 1064 | -4v9e_1_BA | ||
| 1065 | -4v9e_1_BG | ||
| 1066 | -5lzs_1_II | ||
| 1067 | -6fqr_1_C | ||
| 1068 | -6ha1_1_X | ||
| 1069 | -5kcr_1_1X | ||
| 1070 | -6uu4_1_333 | ||
| 1071 | -6uu0_1_333 | ||
| 1072 | -6uuc_1_333 | ||
| 1073 | -6uu2_1_333 | ||
| 1074 | -6xl9_1_R | ||
| 1075 | -6b6h_1_3 | ||
| 1076 | -6xh8_1_3 | ||
| 1077 | -6pb4_1_3 | ||
| 1078 | -3m7n_1_Z | ||
| 1079 | -3m85_1_X | ||
| 1080 | -3m85_1_Z | ||
| 1081 | -3m85_1_Y | ||
| 1082 | -5wnp_1_B | ||
| 1083 | -5wnv_1_B | ||
| 1084 | -5yts_1_B | ||
| 1085 | -1utd_1_6 | ||
| 1086 | -1utd_1_Z | ||
| 1087 | -1utd_1_4 | ||
| 1088 | -1utd_1_7 | ||
| 1089 | -1utd_1_9 | ||
| 1090 | -1utd_1_5 | ||
| 1091 | -1utd_1_3 | ||
| 1092 | -1utd_1_2 | ||
| 1093 | -1utd_1_8 | ||
| 1094 | -1utd_1_1 | ||
| 1095 | -6n6i_1_C | ||
| 1096 | -6n6i_1_D | ||
| 1097 | -6n6a_1_D | ||
| 1098 | -6ij2_1_F | ||
| 1099 | -6ij2_1_G | ||
| 1100 | -6ij2_1_H | ||
| 1101 | -6ij2_1_E | ||
| 1102 | -3u2e_1_D | ||
| 1103 | -3u2e_1_C | ||
| 1104 | -7eh1_1_I | ||
| 1105 | -5uef_1_C | ||
| 1106 | -5uef_1_D | ||
| 1107 | -7eh2_1_R | ||
| 1108 | -7eh2_1_I | ||
| 1109 | -4x4u_1_H | ||
| 1110 | -4afy_1_D | ||
| 1111 | -6oy5_1_I | ||
| 1112 | -6owl_1_B | ||
| 1113 | -6owl_1_C | ||
| 1114 | -4afy_1_C | ||
| 1115 | -4lq3_1_R | ||
| 1116 | -6s0m_1_C | ||
| 1117 | -6ymw_1_C | ||
| 1118 | -7a5g_1_J | ||
| 1119 | -6gx6_1_B | ||
| 1120 | -4k4s_1_D | ||
| 1121 | -4k4s_1_H | ||
| 1122 | -4k4t_1_H | ||
| 1123 | -4k4t_1_D | ||
| 1124 | -1xpu_1_G | ||
| 1125 | -1xpu_1_L | ||
| 1126 | -1xpr_1_L | ||
| 1127 | -1xpu_1_H | ||
| 1128 | -1xpo_1_K | ||
| 1129 | -1xpo_1_J | ||
| 1130 | -1xpu_1_J | ||
| 1131 | -1xpo_1_H | ||
| 1132 | -1xpr_1_J | ||
| 1133 | -1xpu_1_K | ||
| 1134 | -1xpr_1_K | ||
| 1135 | -1xpo_1_M | ||
| 1136 | -1xpo_1_L | ||
| 1137 | -1xpu_1_M | ||
| 1138 | -1xpr_1_M | ||
| 1139 | -1xpo_1_G | ||
| 1140 | -1xpr_1_H | ||
| 1141 | -1xpr_1_G | ||
| 1142 | -5x70_1_E | ||
| 1143 | -5x70_1_G | ||
| 1144 | -6gc5_1_F | ||
| 1145 | -6gc5_1_H | ||
| 1146 | -6gc5_1_G | ||
| 1147 | -1n1h_1_B | ||
| 1148 | -7n2v_1_PT | ||
| 1149 | -4ohz_1_B | ||
| 1150 | -6t83_1_6B | ||
| 1151 | -4gv6_1_C | ||
| 1152 | -4gv6_1_B | ||
| 1153 | -4gv3_1_C | ||
| 1154 | -4gv3_1_B | ||
| 1155 | -4gv9_1_E | ||
| 1156 | -6i7o_1_L | ||
| 1157 | -2a8v_1_D | ||
| 1158 | -6qx3_1_G | ||
| 1159 | -2xnr_1_C | ||
| 1160 | -4gkj_1_W | ||
| 1161 | -5y88_1_X | ||
| 1162 | -3j0o_1_H | ||
| 1163 | -3j0l_1_H | ||
| 1164 | -3j0p_1_H | ||
| 1165 | -3j0q_1_H | ||
| 1166 | -3j0o_1_F | ||
| 1167 | -3j0l_1_F | ||
| 1168 | -3j0p_1_F | ||
| 1169 | -3j0q_1_F | ||
| 1170 | -3j0o_1_B | ||
| 1171 | -3j0l_1_B | ||
| 1172 | -3j0o_1_C | ||
| 1173 | -3j0l_1_C | ||
| 1174 | -3j0q_1_C | ||
| 1175 | -3j0p_1_C | ||
| 1176 | -3j0o_1_A | ||
| 1177 | -3j0l_1_A | ||
| 1178 | -3j0q_1_A | ||
| 1179 | -3j0p_1_A | ||
| 1180 | -6ys3_1_V | ||
| 1181 | -6qdw_1_V | ||
| 1182 | -5hk0_1_F | ||
| 1183 | -4qm6_1_D | ||
| 1184 | -4qm6_1_C | ||
| 1185 | -4jzu_1_C | ||
| 1186 | -4jzv_1_C | ||
| 1187 | -5ytv_1_B | ||
| 1188 | -4k4z_1_P | ||
| 1189 | -4k4z_1_D | ||
| 1190 | -4k4x_1_L | ||
| 1191 | -4k4z_1_L | ||
| 1192 | -4k4x_1_D | ||
| 1193 | -4k4z_1_H | ||
| 1194 | -4k4x_1_H | ||
| 1195 | -4k4x_1_P | ||
| 1196 | -4a3b_1_P | ||
| 1197 | -4a3m_1_P | ||
| 1198 | -6u6y_1_E | ||
| 1199 | -6u6y_1_G | ||
| 1200 | -6u6y_1_F | ||
| 1201 | -6u6y_1_H | ||
| 1202 | -6qik_1_X | ||
| 1203 | -6rzz_1_X | ||
| 1204 | -6ri5_1_X | ||
| 1205 | -6qt0_1_X | ||
| 1206 | -6qtz_1_X | ||
| 1207 | -6s05_1_X | ||
| 1208 | -6t83_1_BB | ||
| 1209 | -6t83_1_4B | ||
| 1210 | -5fl8_1_Z | ||
| 1211 | -5jcs_1_Z | ||
| 1212 | -5mrc_1_BB | ||
| 1213 | -5mre_1_BB | ||
| 1214 | -5mrf_1_BB | ||
| 1215 | -3j46_1_P | ||
| 1216 | -4e6b_1_A | ||
| 1217 | -4e6b_1_B | ||
| 1218 | -6a6l_1_D | ||
| 1219 | -1uvi_1_D | ||
| 1220 | -1uvi_1_F | ||
| 1221 | -1uvi_1_E | ||
| 1222 | -4m7d_1_P | ||
| 1223 | -4k4u_1_D | ||
| 1224 | -4k4u_1_H | ||
| 1225 | -6rt7_1_E | ||
| 1226 | -6rt7_1_A | ||
| 1227 | -2voo_1_C | ||
| 1228 | -2voo_1_D | ||
| 1229 | -5k78_1_X | ||
| 1230 | -5k78_1_Y | ||
| 1231 | -4ylo_1_9 | ||
| 1232 | -5vyc_1_I2 | ||
| 1233 | -5vyc_1_I3 | ||
| 1234 | -5vyc_1_I5 | ||
| 1235 | -5vyc_1_I1 | ||
| 1236 | -5vyc_1_I6 | ||
| 1237 | -5vyc_1_I4 | ||
| 1238 | -6ip8_1_2M | ||
| 1239 | -6ip5_1_2M | ||
| 1240 | -6ip6_1_2M | ||
| 1241 | -6qcs_1_M | ||
| 1242 | -7b5k_1_Z | ||
| 1243 | -4nia_1_O | ||
| 1244 | -4nia_1_J | ||
| 1245 | -4nia_1_K | ||
| 1246 | -4nia_1_L | ||
| 1247 | -4nia_1_F | ||
| 1248 | -4oq9_1_K | ||
| 1249 | -4oq9_1_O | ||
| 1250 | -4oq9_1_J | ||
| 1251 | -4oq9_1_F | ||
| 1252 | -4oq9_1_L | ||
| 1253 | -6r9q_1_B | ||
| 1254 | -7m4u_1_A | ||
| 1255 | -6v3a_1_SN1 | ||
| 1256 | -6v3b_1_SN1 | ||
| 1257 | -6v39_1_SN1 | ||
| 1258 | -6v3e_1_SN1 | ||
| 1259 | -4dr6_1_V | ||
| 1260 | -6kql_1_I | ||
| 1261 | -4eya_1_M | ||
| 1262 | -4eya_1_N | ||
| 1263 | -4eya_1_A | ||
| 1264 | -4eya_1_B | ||
| 1265 | -2wj8_1_D | ||
| 1266 | -2wj8_1_I | ||
| 1267 | -2wj8_1_L | ||
| 1268 | -2wj8_1_F | ||
| 1269 | -2wj8_1_C | ||
| 1270 | -2wj8_1_Q | ||
| 1271 | -2wj8_1_J | ||
| 1272 | -2wj8_1_P | ||
| 1273 | -2wj8_1_K | ||
| 1274 | -2wj8_1_E | ||
| 1275 | -2wj8_1_T | ||
| 1276 | -2wj8_1_B | ||
| 1277 | -2wj8_1_O | ||
| 1278 | -2wj8_1_N | ||
| 1279 | -2wj8_1_A | ||
| 1280 | -2wj8_1_H | ||
| 1281 | -2wj8_1_R | ||
| 1282 | -2wj8_1_M | ||
| 1283 | -2wj8_1_S | ||
| 1284 | -2wj8_1_G | ||
| 1285 | -4e6b_1_E | ||
| 1286 | -4e6b_1_F | ||
| 1287 | -6p71_1_I | ||
| 1288 | -3pdm_1_R | ||
| 1289 | -5det_1_P | ||
| 1290 | -5els_1_I | ||
| 1291 | -4n2s_1_B | ||
| 1292 | -5fl8_1_Y | ||
| 1293 | -5jcs_1_Y | ||
| 1294 | -4yoe_1_E | ||
| 1295 | -6ow3_1_I | ||
| 1296 | -6ovy_1_I | ||
| 1297 | -6oy6_1_I | ||
| 1298 | -4qvd_1_H | ||
| 1299 | -5gxi_1_B | ||
| 1300 | -7n06_1_G | ||
| 1301 | -7n06_1_H | ||
| 1302 | -7n06_1_I | ||
| 1303 | -7n06_1_J | ||
| 1304 | -7n06_1_K | ||
| 1305 | -7n06_1_L | ||
| 1306 | -7n33_1_G | ||
| 1307 | -7n33_1_H | ||
| 1308 | -7n33_1_I | ||
| 1309 | -7n33_1_J | ||
| 1310 | -7n33_1_K | ||
| 1311 | -7n33_1_L | ||
| 1312 | -5mc6_1_N | ||
| 1313 | -4eya_1_O | ||
| 1314 | -4eya_1_P | ||
| 1315 | -4eya_1_C | ||
| 1316 | -4eya_1_D | ||
| 1317 | -6htq_1_V | ||
| 1318 | -6htq_1_W | ||
| 1319 | -6htq_1_U | ||
| 1320 | -6uu6_1_333 | ||
| 1321 | -5a0v_1_F | ||
| 1322 | -3avt_1_T | ||
| 1323 | -6d1v_1_C | ||
| 1324 | -4s2x_1_B | ||
| 1325 | -4s2y_1_B | ||
| 1326 | -5wnu_1_B | ||
| 1327 | -1vtm_1_R | ||
| 1328 | -5elt_1_F | ||
| 1329 | -5elt_1_E | ||
| 1330 | -6xlj_1_R | ||
| 1331 | -6u9x_1_H | ||
| 1332 | -6u9x_1_K | ||
| 1333 | -5elk_1_R | ||
| 1334 | -6okk_1_G | ||
| 1335 | -4cxg_1_A | ||
| 1336 | -4cxh_1_A | ||
| 1337 | -6bk8_1_I | ||
| 1338 | -4cxg_1_B | ||
| 1339 | -4cxh_1_B | ||
| 1340 | -5z4d_1_B | ||
| 1341 | -6o78_1_E | ||
| 1342 | -6xa1_1_BV | ||
| 1343 | -6ha8_1_X | ||
| 1344 | -1m8w_1_E | ||
| 1345 | -1m8w_1_F | ||
| 1346 | -5udi_1_B | ||
| 1347 | -5udl_1_B | ||
| 1348 | -5udk_1_B | ||
| 1349 | -5udj_1_B | ||
| 1350 | -5w5i_1_B | ||
| 1351 | -5w5i_1_D | ||
| 1352 | -5w5h_1_B | ||
| 1353 | -5w5h_1_D | ||
| 1354 | -4eya_1_K | ||
| 1355 | -4eya_1_L | ||
| 1356 | -4eya_1_I | ||
| 1357 | -4eya_1_J | ||
| 1358 | -4g9z_1_E | ||
| 1359 | -4g9z_1_F | ||
| 1360 | -3nma_1_B | ||
| 1361 | -3nma_1_C | ||
| 1362 | -6een_1_G | ||
| 1363 | -6een_1_I | ||
| 1364 | -6een_1_H | ||
| 1365 | -4wti_1_T | ||
| 1366 | -4wti_1_P | ||
| 1367 | -5l3p_1_Y | ||
| 1368 | -4hor_1_X | ||
| 1369 | -3rzo_1_R | ||
| 1370 | -2f4v_1_Z | ||
| 1371 | -1qln_1_R | ||
| 1372 | -3cw1_1_X | ||
| 1373 | -3cw1_1_W | ||
| 1374 | -7b0y_1_A | ||
| 1375 | -6ogy_1_M | ||
| 1376 | -6ogy_1_N | ||
| 1377 | -6uej_1_B | ||
| 1378 | -6ywy_1_BB | ||
| 1379 | -5ytx_1_B | ||
| 1380 | -4g0a_1_H | ||
| 1381 | -6r9p_1_B | ||
| 1382 | -3koa_1_C | ||
| 1383 | -4n48_1_D | ||
| 1384 | -4n48_1_G | ||
| 1385 | -6kug_1_B | ||
| 1386 | -6ktc_1_V | ||
| 1387 | -6ole_1_U | ||
| 1388 | -6om0_1_U | ||
| 1389 | -6olg_1_BV | ||
| 1390 | -6oli_1_U | ||
| 1391 | -6om7_1_U | ||
| 1392 | -6w6l_1_U | ||
| 1393 | -6olz_1_BV | ||
| 1394 | -6olf_1_U | ||
| 1395 | -5lzd_1_X | ||
| 1396 | -6m7k_1_B | ||
| 1397 | -3cd6_1_4 | ||
| 1398 | -3cma_1_5 | ||
| 1399 | -6n9e_1_2W | ||
| 1400 | -1vqo_1_4 | ||
| 1401 | -1qvg_1_3 | ||
| 1402 | -3cme_1_5 | ||
| 1403 | -5lzd_1_W | ||
| 1404 | -5lze_1_W | ||
| 1405 | -5lzc_1_W | ||
| 1406 | -5lzb_1_W | ||
| 1407 | -3wzi_1_C | ||
| 1408 | -1n33_1_Z | ||
| 1409 | -6dti_1_W | ||
| 1410 | -3d2s_1_F | ||
| 1411 | -3d2s_1_H | ||
| 1412 | -5mrc_1_AA | ||
| 1413 | -5mre_1_AA | ||
| 1414 | -5mrf_1_AA | ||
| 1415 | -7jhy_1_Z | ||
| 1416 | -4wkr_1_C | ||
| 1417 | -4v99_1_EC | ||
| 1418 | -4v99_1_AC | ||
| 1419 | -4v99_1_BH | ||
| 1420 | -4v99_1_CH | ||
| 1421 | -4v99_1_AM | ||
| 1422 | -4v99_1_DC | ||
| 1423 | -4v99_1_JW | ||
| 1424 | -4v99_1_EH | ||
| 1425 | -4v99_1_BW | ||
| 1426 | -4v99_1_FW | ||
| 1427 | -4v99_1_AW | ||
| 1428 | -4v99_1_BC | ||
| 1429 | -4v99_1_BM | ||
| 1430 | -4v99_1_IC | ||
| 1431 | -4v99_1_EM | ||
| 1432 | -4v99_1_ER | ||
| 1433 | -4v99_1_IW | ||
| 1434 | -4v99_1_JH | ||
| 1435 | -4v99_1_JR | ||
| 1436 | -4v99_1_AH | ||
| 1437 | -4v99_1_GR | ||
| 1438 | -4v99_1_IR | ||
| 1439 | -4v99_1_BR | ||
| 1440 | -4v99_1_CW | ||
| 1441 | -4v99_1_HR | ||
| 1442 | -4v99_1_FH | ||
| 1443 | -4v99_1_HC | ||
| 1444 | -4v99_1_DW | ||
| 1445 | -4v99_1_GC | ||
| 1446 | -4v99_1_JC | ||
| 1447 | -4v99_1_DM | ||
| 1448 | -4v99_1_EW | ||
| 1449 | -4v99_1_AR | ||
| 1450 | -4v99_1_CR | ||
| 1451 | -4v99_1_JM | ||
| 1452 | -4v99_1_CC | ||
| 1453 | -4v99_1_IH | ||
| 1454 | -4v99_1_FR | ||
| 1455 | -4v99_1_CM | ||
| 1456 | -4v99_1_IM | ||
| 1457 | -4v99_1_FM | ||
| 1458 | -4v99_1_FC | ||
| 1459 | -4v99_1_GH | ||
| 1460 | -4v99_1_HM | ||
| 1461 | -4v99_1_HH | ||
| 1462 | -4v99_1_DR | ||
| 1463 | -4v99_1_HW | ||
| 1464 | -4v99_1_GW | ||
| 1465 | -4v99_1_DH | ||
| 1466 | -4v99_1_GM | ||
| 1467 | -6rt4_1_D | ||
| 1468 | -6rt4_1_C | ||
| 1469 | -6zvh_1_X | ||
| 1470 | -4dwa_1_D | ||
| 1471 | -6n6c_1_D | ||
| 1472 | -6n6j_1_C | ||
| 1473 | -6n6j_1_D | ||
| 1474 | -6p7q_1_E | ||
| 1475 | -6p7q_1_F | ||
| 1476 | -6p7q_1_D | ||
| 1477 | -6rcl_1_C | ||
| 1478 | -5jju_1_C | ||
| 1479 | -4ejt_1_G | ||
| 1480 | -6lkq_1_W | ||
| 1481 | -3qsu_1_P | ||
| 1482 | -3qsu_1_R | ||
| 1483 | -2xs7_1_B | ||
| 1484 | -1n38_1_B | ||
| 1485 | -4qvc_1_G | ||
| 1486 | -6mpf_1_W | ||
| 1487 | -6spc_1_A | ||
| 1488 | -6spe_1_A | ||
| 1489 | -6zvk_1_D2 | ||
| 1490 | -7a01_1_D2 | ||
| 1491 | -6fti_1_V | ||
| 1492 | -6ftj_1_V | ||
| 1493 | -6ftg_1_V | ||
| 1494 | -4g0a_1_G | ||
| 1495 | -4g0a_1_F | ||
| 1496 | -4g0a_1_E | ||
| 1497 | -2b2d_1_S | ||
| 1498 | -5hkc_1_C | ||
| 1499 | -1rmv_1_B | ||
| 1500 | -4qu7_1_X | ||
| 1501 | -4qu7_1_V | ||
| 1502 | -4qu7_1_U | ||
| 1503 | -6pmi_1_3 | ||
| 1504 | -6pmj_1_3 | ||
| 1505 | -5hjz_1_C | ||
| 1506 | 6ydp_1_AA_1176-2737 | 1 | 6ydp_1_AA_1176-2737 |
| 1507 | 6ydw_1_AA_1176-2737 | 2 | 6ydw_1_AA_1176-2737 |
| 1508 | 7d1a_1_A_805-902 | 3 | 7d1a_1_A_805-902 |
| ... | @@ -1514,18 +9,18 @@ | ... | @@ -1514,18 +9,18 @@ |
| 1514 | 7o7z_1_AH_144-220 | 9 | 7o7z_1_AH_144-220 |
| 1515 | 4c9d_1_D_29-1 | 10 | 4c9d_1_D_29-1 |
| 1516 | 4c9d_1_C_29-1 | 11 | 4c9d_1_C_29-1 |
| 1517 | -7aih_1_1_2400-2963 | ||
| 1518 | 7aih_1_1_2984-3610 | 12 | 7aih_1_1_2984-3610 |
| 1519 | -7ane_1_2_1904-2468 | 13 | +7aih_1_1_2400-2963 |
| 1520 | 7ane_1_2_2489-3115 | 14 | 7ane_1_2_2489-3115 |
| 15 | +7ane_1_2_1904-2468 | ||
| 1521 | 5g2x_1_A_595-692 | 16 | 5g2x_1_A_595-692 |
| 1522 | -7aor_1_2_2020-2579 | ||
| 1523 | 7aor_1_2_2589-3210 | 17 | 7aor_1_2_2589-3210 |
| 18 | +7aor_1_2_2020-2579 | ||
| 1524 | 7a5p_1_2_259-449 | 19 | 7a5p_1_2_259-449 |
| 1525 | -7aor_1_A_2020-2579 | ||
| 1526 | 7aor_1_A_2589-3210 | 20 | 7aor_1_A_2589-3210 |
| 1527 | -7am2_1_1_1904-2470 | 21 | +7aor_1_A_2020-2579 |
| 1528 | 7am2_1_1_2491-3117 | 22 | 7am2_1_1_2491-3117 |
| 1529 | -7ane_1_1_1904-2468 | 23 | +7am2_1_1_1904-2470 |
| 1530 | 7ane_1_1_2489-3115 | 24 | 7ane_1_1_2489-3115 |
| 25 | +7ane_1_1_1904-2468 | ||
| 1531 | 6uz7_1_8_2140-2825 | 26 | 6uz7_1_8_2140-2825 | ... | ... |
This diff could not be displayed because it is too large.
| ... | @@ -920,14 +920,22 @@ def general_stats(): | ... | @@ -920,14 +920,22 @@ def general_stats(): |
| 920 | 920 | ||
| 921 | @trace_unhandled_exceptions | 921 | @trace_unhandled_exceptions |
| 922 | def par_distance_matrix(filelist, f, label, cm_coords, consider_all_atoms, s): | 922 | def par_distance_matrix(filelist, f, label, cm_coords, consider_all_atoms, s): |
| 923 | - | 923 | + """ |
| 924 | + Get the pairwise distances in one 3D molecule, given its aligned sequence (with gaps). | ||
| 925 | + Returns a tuple of numpy arrays: | ||
| 926 | + - The first is a boolean matrix, whose values are 1 if the distance is NaN (unresolved residue, or missing atom...), 0 otherwise | ||
| 927 | + - The second is the distance matrix (in angströms), unresolved positions are 0 (not NaN) | ||
| 928 | + - The third is the square of the second (square-distance matrix), unresolved positions are 0 (not NaN) | ||
| 929 | + """ | ||
| 930 | + | ||
| 924 | # Identify the right 3D file | 931 | # Identify the right 3D file |
| 925 | - filename = '' | 932 | + filename = "" |
| 926 | for file in filelist: | 933 | for file in filelist: |
| 927 | if file.startswith(s.id.split("RF")[0].replace('-', '').replace('[', '_').replace(']', '_')): | 934 | if file.startswith(s.id.split("RF")[0].replace('-', '').replace('[', '_').replace(']', '_')): |
| 928 | filename = path_to_3D_data + "rna_mapped_to_Rfam/" + file | 935 | filename = path_to_3D_data + "rna_mapped_to_Rfam/" + file |
| 929 | break | 936 | break |
| 930 | if not len(filename): | 937 | if not len(filename): |
| 938 | + # chain is not in file list. Maybe you are in non-redundant mode and it is not a representative (normal case). | ||
| 931 | return None, None, None | 939 | return None, None, None |
| 932 | 940 | ||
| 933 | # Get the coordinates of every existing nt in the 3D file | 941 | # Get the coordinates of every existing nt in the 3D file |
| ... | @@ -938,9 +946,9 @@ def par_distance_matrix(filelist, f, label, cm_coords, consider_all_atoms, s): | ... | @@ -938,9 +946,9 @@ def par_distance_matrix(filelist, f, label, cm_coords, consider_all_atoms, s): |
| 938 | warn("No C1' atoms in " + filename.split('/')[-1] + ", ignoring") | 946 | warn("No C1' atoms in " + filename.split('/')[-1] + ", ignoring") |
| 939 | return None, None, None | 947 | return None, None, None |
| 940 | except FileNotFoundError: | 948 | except FileNotFoundError: |
| 949 | + warn(f"{label} not found in the mapped mmCIF files") | ||
| 941 | return None, None, None | 950 | return None, None, None |
| 942 | 951 | ||
| 943 | - | ||
| 944 | # Get the coordinates of every position in the alignment | 952 | # Get the coordinates of every position in the alignment |
| 945 | nb_gap = 0 | 953 | nb_gap = 0 |
| 946 | coordinates_with_gaps = [] | 954 | coordinates_with_gaps = [] |
| ... | @@ -965,7 +973,6 @@ def par_distance_matrix(filelist, f, label, cm_coords, consider_all_atoms, s): | ... | @@ -965,7 +973,6 @@ def par_distance_matrix(filelist, f, label, cm_coords, consider_all_atoms, s): |
| 965 | d[i,j] = get_euclidian_distance(coordinates_with_gaps[i], coordinates_with_gaps[j]) | 973 | d[i,j] = get_euclidian_distance(coordinates_with_gaps[i], coordinates_with_gaps[j]) |
| 966 | 974 | ||
| 967 | # Save the individual distance matrices | 975 | # Save the individual distance matrices |
| 968 | - # if f not in LSU_set and f not in SSU_set: | ||
| 969 | np.savetxt(runDir + '/results/distance_matrices/' + f + '_'+ label + '/'+ s.id.strip("\'") + '.csv', d, delimiter=",", fmt="%.3f") | 976 | np.savetxt(runDir + '/results/distance_matrices/' + f + '_'+ label + '/'+ s.id.strip("\'") + '.csv', d, delimiter=",", fmt="%.3f") |
| 970 | 977 | ||
| 971 | # For the average and sd, we want to consider only positions of the consensus model. This means: | 978 | # For the average and sd, we want to consider only positions of the consensus model. This means: |
| ... | @@ -979,7 +986,7 @@ def par_distance_matrix(filelist, f, label, cm_coords, consider_all_atoms, s): | ... | @@ -979,7 +986,7 @@ def par_distance_matrix(filelist, f, label, cm_coords, consider_all_atoms, s): |
| 979 | while cm_coords[i] is None: | 986 | while cm_coords[i] is None: |
| 980 | i += 1 | 987 | i += 1 |
| 981 | family_start = int(cm_coords[i]) | 988 | family_start = int(cm_coords[i]) |
| 982 | - # c = np.zeros((family_end, family_end), dtype=np.float32) # new matrix of size of the consensus model for the family | 989 | + # new matrix of size of the consensus model for the family |
| 983 | c = np.NaN * np.ones((family_end, family_end), dtype=np.float32) | 990 | c = np.NaN * np.ones((family_end, family_end), dtype=np.float32) |
| 984 | # set to NaN zones that never exist in the 3D data | 991 | # set to NaN zones that never exist in the 3D data |
| 985 | for i in range(family_start-1): | 992 | for i in range(family_start-1): |
| ... | @@ -1000,8 +1007,8 @@ def par_distance_matrix(filelist, f, label, cm_coords, consider_all_atoms, s): | ... | @@ -1000,8 +1007,8 @@ def par_distance_matrix(filelist, f, label, cm_coords, consider_all_atoms, s): |
| 1000 | return 1-np.isnan(c).astype(int), np.nan_to_num(c), np.nan_to_num(c*c) | 1007 | return 1-np.isnan(c).astype(int), np.nan_to_num(c), np.nan_to_num(c*c) |
| 1001 | 1008 | ||
| 1002 | @trace_unhandled_exceptions | 1009 | @trace_unhandled_exceptions |
| 1003 | -def get_avg_std_distance_matrix(f, consider_all_atoms, multithread=False): | 1010 | +def get_avg_std_distance_matrix(f, res, consider_all_atoms=False, redundancy=False, multithread=False): |
| 1004 | - np.seterr(divide='ignore') # ignore division by zero issues | 1011 | + # np.seterr(divide='ignore') # ignore division by zero issues |
| 1005 | 1012 | ||
| 1006 | if consider_all_atoms: | 1013 | if consider_all_atoms: |
| 1007 | label = "base" | 1014 | label = "base" |
| ... | @@ -1009,23 +1016,38 @@ def get_avg_std_distance_matrix(f, consider_all_atoms, multithread=False): | ... | @@ -1009,23 +1016,38 @@ def get_avg_std_distance_matrix(f, consider_all_atoms, multithread=False): |
| 1009 | label = "backbone" | 1016 | label = "backbone" |
| 1010 | 1017 | ||
| 1011 | if not multithread: | 1018 | if not multithread: |
| 1012 | - # This function call is for ONE worker. | 1019 | + # This function call is for ONE worker. Get a worker number for it to position the progress bar. |
| 1013 | - # Get a worker number for it to position the progress bar | ||
| 1014 | global idxQueue | 1020 | global idxQueue |
| 1015 | thr_idx = idxQueue.get() | 1021 | thr_idx = idxQueue.get() |
| 1016 | setproctitle(f"RNANet statistics.py Worker {thr_idx+1} {f} {label} distance matrices") | 1022 | setproctitle(f"RNANet statistics.py Worker {thr_idx+1} {f} {label} distance matrices") |
| 1017 | 1023 | ||
| 1018 | os.makedirs(runDir + '/results/distance_matrices/' + f + '_' + label, exist_ok=True ) | 1024 | os.makedirs(runDir + '/results/distance_matrices/' + f + '_' + label, exist_ok=True ) |
| 1019 | - | 1025 | + |
| 1020 | - align = AlignIO.read(path_to_seq_data + f"realigned/{f}_3d_only.afa", "fasta") | 1026 | + # Get the list of 3D files. They should exist in the folder from the last RNANet run with --extract option. |
| 1021 | - ncols = align.get_alignment_length() | 1027 | + if redundancy: |
| 1028 | + with sqlite3.connect(runDir + "/results/RNANet.db") as conn: | ||
| 1029 | + conn.execute('pragma journal_mode=wal') | ||
| 1030 | + r = sql_ask_database(conn, f"SELECT structure_id, '_1_', chain_name, '_', CAST(pdb_start AS TEXT), '-', CAST(pdb_end AS TEXT) FROM chain WHERE rfam_acc='{f}' AND issue=0;") | ||
| 1031 | + filelist = sorted([ ''.join(list(x))+'.cif' for x in r ]) | ||
| 1032 | + else: | ||
| 1033 | + filelist = sorted(representatives_from_nrlist(res, mapped_to=f)) | ||
| 1034 | + | ||
| 1035 | + # Open the 3D-only alignment. keep only files that will be considered in 3D (e.g. representatives) | ||
| 1036 | + temp_align = AlignIO.read(path_to_seq_data + f"realigned/{f}_3d_only.afa", "fasta") | ||
| 1037 | + align = [] | ||
| 1038 | + for s in temp_align: | ||
| 1039 | + filename = "" | ||
| 1040 | + for file in filelist: | ||
| 1041 | + if file.startswith(s.id.split("RF")[0].replace('-', '').replace('[', '_').replace(']', '_')): | ||
| 1042 | + align.append(s) | ||
| 1043 | + break | ||
| 1044 | + ncols = temp_align.get_alignment_length() | ||
| 1022 | found = 0 | 1045 | found = 0 |
| 1023 | notfound = 0 | 1046 | notfound = 0 |
| 1047 | + | ||
| 1024 | # retrieve the mappings between this family's alignment and the CM model: | 1048 | # retrieve the mappings between this family's alignment and the CM model: |
| 1025 | with sqlite3.connect(runDir + "/results/RNANet.db") as conn: | 1049 | with sqlite3.connect(runDir + "/results/RNANet.db") as conn: |
| 1026 | conn.execute('pragma journal_mode=wal') | 1050 | conn.execute('pragma journal_mode=wal') |
| 1027 | - r = sql_ask_database(conn, f"SELECT structure_id, '_1_', chain_name, '_', CAST(pdb_start AS TEXT), '-', CAST(pdb_end AS TEXT) FROM chain WHERE rfam_acc='{f}';") | ||
| 1028 | - filelist = sorted([ ''.join(list(x))+'.cif' for x in r ]) | ||
| 1029 | r = sql_ask_database(conn, f"SELECT cm_coord FROM align_column WHERE rfam_acc = '{f}' AND index_ali > 0 ORDER BY index_ali ASC;") | 1051 | r = sql_ask_database(conn, f"SELECT cm_coord FROM align_column WHERE rfam_acc = '{f}' AND index_ali > 0 ORDER BY index_ali ASC;") |
| 1030 | cm_coords = [ x[0] for x in r ] # len(cm_coords) is the number of saved columns. There are many None values in the list. | 1052 | cm_coords = [ x[0] for x in r ] # len(cm_coords) is the number of saved columns. There are many None values in the list. |
| 1031 | i = len(cm_coords)-1 | 1053 | i = len(cm_coords)-1 |
| ... | @@ -1042,7 +1064,7 @@ def get_avg_std_distance_matrix(f, consider_all_atoms, multithread=False): | ... | @@ -1042,7 +1064,7 @@ def get_avg_std_distance_matrix(f, consider_all_atoms, multithread=False): |
| 1042 | counts = np.zeros((family_end, family_end)) | 1064 | counts = np.zeros((family_end, family_end)) |
| 1043 | avg = np.zeros((family_end, family_end)) | 1065 | avg = np.zeros((family_end, family_end)) |
| 1044 | std = np.zeros((family_end, family_end)) | 1066 | std = np.zeros((family_end, family_end)) |
| 1045 | - | 1067 | + |
| 1046 | if not multithread: | 1068 | if not multithread: |
| 1047 | pbar = tqdm(total = len(align), position=thr_idx+1, desc=f"Worker {thr_idx+1}: {f} {label} distance matrices", unit="chains", leave=False) | 1069 | pbar = tqdm(total = len(align), position=thr_idx+1, desc=f"Worker {thr_idx+1}: {f} {label} distance matrices", unit="chains", leave=False) |
| 1048 | pbar.update(0) | 1070 | pbar.update(0) |
| ... | @@ -1054,16 +1076,15 @@ def get_avg_std_distance_matrix(f, consider_all_atoms, multithread=False): | ... | @@ -1054,16 +1076,15 @@ def get_avg_std_distance_matrix(f, consider_all_atoms, multithread=False): |
| 1054 | avg += d | 1076 | avg += d |
| 1055 | std += dsquared | 1077 | std += dsquared |
| 1056 | else: | 1078 | else: |
| 1079 | + # d is None means the considered RNA is not in the filelist (e.g., not a representative), or is not found. | ||
| 1057 | notfound += 1 | 1080 | notfound += 1 |
| 1058 | pbar.update(1) | 1081 | pbar.update(1) |
| 1059 | pbar.close() | 1082 | pbar.close() |
| 1060 | else: | 1083 | else: |
| 1061 | # We split the work for one family on multiple workers. | 1084 | # We split the work for one family on multiple workers. |
| 1062 | - | ||
| 1063 | p = Pool(initializer=init_with_tqdm, initargs=(tqdm.get_lock(),), processes=nworkers) | 1085 | p = Pool(initializer=init_with_tqdm, initargs=(tqdm.get_lock(),), processes=nworkers) |
| 1064 | try: | 1086 | try: |
| 1065 | fam_pbar = tqdm(total=len(align), desc=f"{f} {label} pair distances", position=0, unit="chain", leave=True) | 1087 | fam_pbar = tqdm(total=len(align), desc=f"{f} {label} pair distances", position=0, unit="chain", leave=True) |
| 1066 | - # Apply work_pssm_remap to each RNA family | ||
| 1067 | for i, (contrib, d, dsquared) in enumerate(p.imap_unordered(partial(par_distance_matrix, filelist, f, label, cm_coords, consider_all_atoms), align, chunksize=1)): | 1088 | for i, (contrib, d, dsquared) in enumerate(p.imap_unordered(partial(par_distance_matrix, filelist, f, label, cm_coords, consider_all_atoms), align, chunksize=1)): |
| 1068 | if d is not None: | 1089 | if d is not None: |
| 1069 | found += 1 | 1090 | found += 1 |
| ... | @@ -1128,15 +1149,15 @@ def get_avg_std_distance_matrix(f, consider_all_atoms, multithread=False): | ... | @@ -1128,15 +1149,15 @@ def get_avg_std_distance_matrix(f, consider_all_atoms, multithread=False): |
| 1128 | if not multithread: | 1149 | if not multithread: |
| 1129 | idxQueue.put(thr_idx) # replace the thread index in the queue | 1150 | idxQueue.put(thr_idx) # replace the thread index in the queue |
| 1130 | setproctitle(f"RNANet statistics.py Worker {thr_idx+1} finished") | 1151 | setproctitle(f"RNANet statistics.py Worker {thr_idx+1} finished") |
| 1131 | - else: | 1152 | + # else: |
| 1132 | - # basically, for the rRNAs | 1153 | + # # basically, for the rRNAs |
| 1133 | - # we delete the unique csv files for each chain, they wheight hundreds of gigabytes together | 1154 | + # # we delete the unique csv files for each chain, they wheight hundreds of gigabytes together |
| 1134 | - warn(f"Removing {f} ({label}) individual distance matrices, they weight too much. keeping the averages and standard deviations.") | 1155 | + # warn(f"Removing {f} ({label}) individual distance matrices, they weight too much. keeping the averages and standard deviations.") |
| 1135 | - for csv in glob.glob(runDir + '/results/distance_matrices/' + f + '_'+ label + "/*-" + f + ".csv"): | 1156 | + # for csv in glob.glob(runDir + '/results/distance_matrices/' + f + '_'+ label + "/*-" + f + ".csv"): |
| 1136 | - try: | 1157 | + # try: |
| 1137 | - os.remove(csv) | 1158 | + # os.remove(csv) |
| 1138 | - except FileNotFoundError: | 1159 | + # except FileNotFoundError: |
| 1139 | - pass | 1160 | + # pass |
| 1140 | return 0 | 1161 | return 0 |
| 1141 | 1162 | ||
| 1142 | @trace_unhandled_exceptions | 1163 | @trace_unhandled_exceptions |
| ... | @@ -1195,7 +1216,7 @@ def nt_3d_centers(cif_file, consider_all_atoms): | ... | @@ -1195,7 +1216,7 @@ def nt_3d_centers(cif_file, consider_all_atoms): |
| 1195 | try: | 1216 | try: |
| 1196 | structure = MMCIFParser().get_structure(cif_file, cif_file) | 1217 | structure = MMCIFParser().get_structure(cif_file, cif_file) |
| 1197 | except Exception as e: | 1218 | except Exception as e: |
| 1198 | - warn(f"{cif_file.split('/')[-1]} : {e}", error=True) | 1219 | + warn(f"\n{cif_file.split('/')[-1]} : {e}", error=True) |
| 1199 | with open(runDir + "/errors.txt", "a") as f: | 1220 | with open(runDir + "/errors.txt", "a") as f: |
| 1200 | f.write(f"Exception in nt_3d_centers({cif_file.split('/')[-1]})\n") | 1221 | f.write(f"Exception in nt_3d_centers({cif_file.split('/')[-1]})\n") |
| 1201 | f.write(str(e)) | 1222 | f.write(str(e)) |
| ... | @@ -1225,24 +1246,54 @@ def nt_3d_centers(cif_file, consider_all_atoms): | ... | @@ -1225,24 +1246,54 @@ def nt_3d_centers(cif_file, consider_all_atoms): |
| 1225 | result.append(res) | 1246 | result.append(res) |
| 1226 | return(result) | 1247 | return(result) |
| 1227 | 1248 | ||
| 1228 | -def representatives_from_nrlist(res): | 1249 | +def representatives_from_nrlist(res, mapped_to=None): |
| 1250 | + """ | ||
| 1251 | + Returns the list of filenames corresponding to the 3D cif files of structures | ||
| 1252 | + that represent a "cluster" (a redundancy class) at the given resolution. | ||
| 1253 | + | ||
| 1254 | + If mapped is not None, then the database is searched for a mapping to a family. | ||
| 1255 | + """ | ||
| 1256 | + | ||
| 1257 | + # Read the NR file | ||
| 1229 | nr_code = min([i for i in [1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 20.0] if i >= res]) | 1258 | nr_code = min([i for i in [1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 20.0] if i >= res]) |
| 1230 | - fpath = f"/home/data/RNA/3D/latest_nr_list_{nr_code}A.csv" | 1259 | + fpath = f"{path_to_3D_data}/latest_nr_list_{nr_code}A.csv" |
| 1231 | repres = [] | 1260 | repres = [] |
| 1232 | df = pd.read_csv(os.path.abspath(fpath)) | 1261 | df = pd.read_csv(os.path.abspath(fpath)) |
| 1262 | + | ||
| 1263 | + # define a function to transform a code into a filename | ||
| 1264 | + def query_mapping_to(structure, model, chain, family): | ||
| 1265 | + if family is None: | ||
| 1266 | + return structure + '_' + model + '_' + chain + ".cif" | ||
| 1267 | + | ||
| 1268 | + # if we need a mapping start and end, query database | ||
| 1269 | + with sqlite3.connect(runDir + "/results/RNANet.db") as conn: | ||
| 1270 | + conn.execute('pragma journal_mode=wal') | ||
| 1271 | + r = sql_ask_database(conn, f"SELECT pdb_start, pdb_end FROM chain WHERE rfam_acc='{family}' AND structure_id='{structure}' AND chain_name='{chain}' AND issue=0;") | ||
| 1272 | + | ||
| 1273 | + if not len(r): | ||
| 1274 | + # there is no chain named like this and mapped to this family | ||
| 1275 | + return None | ||
| 1276 | + | ||
| 1277 | + if len(r) > 1: | ||
| 1278 | + warn(f"Several entries found for structure {structure}-{chain} ({family}) : {len(r)} entries") | ||
| 1279 | + return structure + '_' + model + '_' + chain + '_' + str(r[0][0]) + '-' + str(r[0][1]) + ".cif" | ||
| 1280 | + | ||
| 1281 | + # build the list | ||
| 1233 | for i in range(df.shape[0]): | 1282 | for i in range(df.shape[0]): |
| 1234 | up_name = df["representative"][i] | 1283 | up_name = df["representative"][i] |
| 1235 | if '+' in up_name: | 1284 | if '+' in up_name: |
| 1236 | up_name = up_name.split('+') | 1285 | up_name = up_name.split('+') |
| 1237 | for i in range(len(up_name)): | 1286 | for i in range(len(up_name)): |
| 1238 | chain = up_name[i].split('|') | 1287 | chain = up_name[i].split('|') |
| 1239 | - chain = chain[0].lower() + '_' + chain[1] + '_' + chain[2] | 1288 | + reference = query_mapping_to(chain[0].lower(), chain[1], chain[2], mapped_to) |
| 1240 | - repres.append(chain + '.cif') | 1289 | + if reference is not None: |
| 1290 | + repres.append(reference) | ||
| 1241 | else : | 1291 | else : |
| 1242 | up_name = up_name.split('|') | 1292 | up_name = up_name.split('|') |
| 1243 | - low_name = up_name[0].lower() + '_' + up_name[1] + '_' + up_name[2] | 1293 | + reference = query_mapping_to(up_name[0].lower(), up_name[1], up_name[2], mapped_to) |
| 1244 | - repres.append(low_name + '.cif') | 1294 | + if reference is not None: |
| 1245 | - | 1295 | + repres.append(reference) |
| 1296 | + | ||
| 1246 | return repres | 1297 | return repres |
| 1247 | 1298 | ||
| 1248 | def log_to_pbar(pbar): | 1299 | def log_to_pbar(pbar): |
| ... | @@ -1281,11 +1332,12 @@ if __name__ == "__main__": | ... | @@ -1281,11 +1332,12 @@ if __name__ == "__main__": |
| 1281 | DELETE_OLD_DATA = False | 1332 | DELETE_OLD_DATA = False |
| 1282 | DO_WADLEY_ANALYSIS = False | 1333 | DO_WADLEY_ANALYSIS = False |
| 1283 | DO_AVG_DISTANCE_MATRIX = False | 1334 | DO_AVG_DISTANCE_MATRIX = False |
| 1335 | + REDUNDANT_DIST_MAT = True | ||
| 1284 | DO_HIRE_RNA_MEASURES = False | 1336 | DO_HIRE_RNA_MEASURES = False |
| 1285 | RESCAN_GMM_COMP_NUM = False | 1337 | RESCAN_GMM_COMP_NUM = False |
| 1286 | try: | 1338 | try: |
| 1287 | opts, _ = getopt.getopt( sys.argv[1:], "r:h", | 1339 | opts, _ = getopt.getopt( sys.argv[1:], "r:h", |
| 1288 | - [ "help", "from-scratch", "wadley", "distance-matrices", "resolution=", | 1340 | + [ "help", "from-scratch", "wadley", "distance-matrices", "non-redundant", "resolution=", |
| 1289 | "3d-folder=", "seq-folder=", "hire-rna", "rescan-nmodes" ]) | 1341 | "3d-folder=", "seq-folder=", "hire-rna", "rescan-nmodes" ]) |
| 1290 | except getopt.GetoptError as err: | 1342 | except getopt.GetoptError as err: |
| 1291 | print(err) | 1343 | print(err) |
| ... | @@ -1301,14 +1353,17 @@ if __name__ == "__main__": | ... | @@ -1301,14 +1353,17 @@ if __name__ == "__main__": |
| 1301 | print() | 1353 | print() |
| 1302 | print("-r 20.0 [ --resolution=20.0 ]\tCompute statistics using chains of resolution 20.0A or better.") | 1354 | print("-r 20.0 [ --resolution=20.0 ]\tCompute statistics using chains of resolution 20.0A or better.") |
| 1303 | print("--3d-folder=…\t\t\tPath to a folder containing the 3D data files. Required subfolders should be:" | 1355 | print("--3d-folder=…\t\t\tPath to a folder containing the 3D data files. Required subfolders should be:" |
| 1304 | - "\n\t\t\t\t\tdatapoints/\t\tFinal results in CSV file format.") | 1356 | + "\n\t\t\t\t\tdatapoints/\t\tFinal results in CSV file format." |
| 1357 | + "\n\t\t\t\t\trna_mapped_to_Rfam/\tmmCIF files produced by RNANet (using --extract)." | ||
| 1358 | + "\n\t\t\t\t\trna_only/\t\tmmCIF files produced by RNANet in no-homology mode.") | ||
| 1305 | print("--seq-folder=…\t\t\tPath to a folder containing the sequence and alignment files. Required subfolder:" | 1359 | print("--seq-folder=…\t\t\tPath to a folder containing the sequence and alignment files. Required subfolder:" |
| 1306 | "\n\t\t\t\t\trealigned/\t\tSequences, covariance models, and alignments by family") | 1360 | "\n\t\t\t\t\trealigned/\t\tSequences, covariance models, and alignments by family") |
| 1307 | print("--from-scratch\t\t\tDo not use precomputed results from past runs, recompute everything") | 1361 | print("--from-scratch\t\t\tDo not use precomputed results from past runs, recompute everything") |
| 1308 | print("--distance-matrices\t\tCompute average distance between nucleotide pairs for each family.") | 1362 | print("--distance-matrices\t\tCompute average distance between nucleotide pairs for each family.") |
| 1363 | + print("--non-redundant\t\t\tIn distance matrix computation, only use the equivalence class representatives.\n\t\t\t\t Does not apply to rRNAs, where the option is always True.") | ||
| 1309 | print("--wadley\t\t\tReproduce Wadley & al 2007 clustering of pseudotorsions.") | 1364 | print("--wadley\t\t\tReproduce Wadley & al 2007 clustering of pseudotorsions.") |
| 1310 | - print("--hire-rna\t\t\tCompute distances between atoms and torsion angles for HiRE-RNA model, and plot GMMs on the data.") | 1365 | + print("--hire-rna\t\t\tCompute distances between atoms and torsion angles for HiRE-RNA model,\n\t\t\t\t and plot GMMs on the data.") |
| 1311 | - print("--rescan-nmodes\t\tDo not assume the number of modes in distances and angles distributions, measure it.") | 1366 | + print("--rescan-nmodes\t\t\tDo not assume the number of modes in distances and angles distributions, measure it.") |
| 1312 | sys.exit() | 1367 | sys.exit() |
| 1313 | elif opt == "--version": | 1368 | elif opt == "--version": |
| 1314 | print("RNANet statistics 1.6 beta") | 1369 | print("RNANet statistics 1.6 beta") |
| ... | @@ -1350,6 +1405,8 @@ if __name__ == "__main__": | ... | @@ -1350,6 +1405,8 @@ if __name__ == "__main__": |
| 1350 | os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/basepairs/", exist_ok=True) | 1405 | os.makedirs(runDir + "/results/figures/GMM/HiRE-RNA/basepairs/", exist_ok=True) |
| 1351 | elif opt == "--rescan-nmodes": | 1406 | elif opt == "--rescan-nmodes": |
| 1352 | RESCAN_GMM_COMP_NUM = True | 1407 | RESCAN_GMM_COMP_NUM = True |
| 1408 | + elif opt == "--non-redundant": | ||
| 1409 | + REDUNDANT_DIST_MAT = False | ||
| 1353 | 1410 | ||
| 1354 | # Load mappings. famlist will contain only families with structures at this resolution threshold. | 1411 | # Load mappings. famlist will contain only families with structures at this resolution threshold. |
| 1355 | 1412 | ||
| ... | @@ -1373,7 +1430,7 @@ if __name__ == "__main__": | ... | @@ -1373,7 +1430,7 @@ if __name__ == "__main__": |
| 1373 | ignored = families[families.n_chains < 3].rfam_acc.tolist() | 1430 | ignored = families[families.n_chains < 3].rfam_acc.tolist() |
| 1374 | famlist.sort(key=family_order) | 1431 | famlist.sort(key=family_order) |
| 1375 | 1432 | ||
| 1376 | - print(f"Found {len(famlist)} families with chains of resolution {res_thr}A or better.") | 1433 | + print(f"Found {len(famlist)} families with chains or better.") |
| 1377 | if len(ignored): | 1434 | if len(ignored): |
| 1378 | print(f"Idty matrices: Ignoring {len(ignored)} families with only one chain:", " ".join(ignored)+'\n') | 1435 | print(f"Idty matrices: Ignoring {len(ignored)} families with only one chain:", " ".join(ignored)+'\n') |
| 1379 | 1436 | ||
| ... | @@ -1413,8 +1470,8 @@ if __name__ == "__main__": | ... | @@ -1413,8 +1470,8 @@ if __name__ == "__main__": |
| 1413 | e3 = file.split('_')[2] | 1470 | e3 = file.split('_')[2] |
| 1414 | extracted_chains.append(e1 + '[' + e2 + ']' + '-' + e3) | 1471 | extracted_chains.append(e1 + '[' + e2 + ']' + '-' + e3) |
| 1415 | for f in [ x for x in famlist if (x not in LSU_set and x not in SSU_set) ]: # Process the rRNAs later only 3 by 3 | 1472 | for f in [ x for x in famlist if (x not in LSU_set and x not in SSU_set) ]: # Process the rRNAs later only 3 by 3 |
| 1416 | - joblist.append(Job(function=get_avg_std_distance_matrix, args=(f, True, False))) | 1473 | + joblist.append(Job(function=get_avg_std_distance_matrix, args=(f, res_thr, True, REDUNDANT_DIST_MAT, False))) |
| 1417 | - joblist.append(Job(function=get_avg_std_distance_matrix, args=(f, False, False))) | 1474 | + joblist.append(Job(function=get_avg_std_distance_matrix, args=(f, res_thr, False, REDUNDANT_DIST_MAT, False))) |
| 1418 | 1475 | ||
| 1419 | # Do general family statistics | 1476 | # Do general family statistics |
| 1420 | joblist.append(Job(function=stats_len)) # Computes figures about chain lengths | 1477 | joblist.append(Job(function=stats_len)) # Computes figures about chain lengths |
| ... | @@ -1428,7 +1485,6 @@ if __name__ == "__main__": | ... | @@ -1428,7 +1485,6 @@ if __name__ == "__main__": |
| 1428 | # Do geometric measures | 1485 | # Do geometric measures |
| 1429 | if n_unmapped_chains: | 1486 | if n_unmapped_chains: |
| 1430 | os.makedirs(runDir + "/results/geometry/all-atoms/distances/", exist_ok=True) | 1487 | os.makedirs(runDir + "/results/geometry/all-atoms/distances/", exist_ok=True) |
| 1431 | - # structure_list = os.listdir(path_to_3D_data + "rna_only") | ||
| 1432 | structure_list = representatives_from_nrlist(res_thr) | 1488 | structure_list = representatives_from_nrlist(res_thr) |
| 1433 | for f in structure_list: | 1489 | for f in structure_list: |
| 1434 | if path.isfile(path_to_3D_data + "datapoints/" + f.split('.')[0]): | 1490 | if path.isfile(path_to_3D_data + "datapoints/" + f.split('.')[0]): |
| ... | @@ -1438,12 +1494,17 @@ if __name__ == "__main__": | ... | @@ -1438,12 +1494,17 @@ if __name__ == "__main__": |
| 1438 | 1494 | ||
| 1439 | # Now process the memory-heavy tasks family by family | 1495 | # Now process the memory-heavy tasks family by family |
| 1440 | if DO_AVG_DISTANCE_MATRIX: | 1496 | if DO_AVG_DISTANCE_MATRIX: |
| 1497 | + print("Computing distances matrices of rRNA families using only the equivalence class representatives, for storage purposes.") | ||
| 1498 | + # Note that, if the user has more than 300 GB of free storage space, one could use all the rRNAs. | ||
| 1499 | + # Yes, within an equivalence class, the rRNA molecules are close in sequence and structure. | ||
| 1500 | + # But yet, having several 3D structures of the same molecule gives an insight about structure flexibility in some regions. | ||
| 1501 | + # Detect free space automatically ? TODISCUSS + TODECIDE + TODO | ||
| 1441 | for f in LSU_set: | 1502 | for f in LSU_set: |
| 1442 | - get_avg_std_distance_matrix(f, True, True) | 1503 | + get_avg_std_distance_matrix(f, res_thr, True, False, True) |
| 1443 | - get_avg_std_distance_matrix(f, False, True) | 1504 | + get_avg_std_distance_matrix(f, res_thr, False, False, True) |
| 1444 | for f in SSU_set: | 1505 | for f in SSU_set: |
| 1445 | - get_avg_std_distance_matrix(f, True, True) | 1506 | + get_avg_std_distance_matrix(f, res_thr, True, False, True) |
| 1446 | - get_avg_std_distance_matrix(f, False, True) | 1507 | + get_avg_std_distance_matrix(f, res_thr, False, False, True) |
| 1447 | 1508 | ||
| 1448 | print() | 1509 | print() |
| 1449 | print() | 1510 | print() |
| ... | @@ -1477,3 +1538,4 @@ if __name__ == "__main__": | ... | @@ -1477,3 +1538,4 @@ if __name__ == "__main__": |
| 1477 | process_jobs(joblist) | 1538 | process_jobs(joblist) |
| 1478 | merge_jsons() | 1539 | merge_jsons() |
| 1479 | 1540 | ||
| 1541 | + | ... | ... |
-
mentioned in commit 0487812b
-
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