tests/testthat/_snaps/extract_from_hmmer.md

Test that extract hmmer works with phmmer and pdb for extract pdbs using phmmer

Code
  .
Output
        pdbs
  1   2abl_A
  2   2fo0_A
  3   5mo4_A
  4   1opk_A
  5   1opl_B
  6   6amw_A
  7   1ju5_C
  8   1bbz_G
  9   1abo_A
  10  4j9h_F
  11  5np2_B
  12  3eg0_A
  13  3eg2_A
  14  2o88_A
  15  1awo_A
  16  3egu_A
  17  4j9b_A
  18  5np3_C
  19  5dc9_A
  20  5dc0_B
  21  1ab2_A
  22  2ecd_A
  23  4eih_A
  24  3uf4_A
  25  1g83_B
  26  4xey_A
  27  3k2m_B
  28  4xi2_A
  29  2yt6_A
  30  4ag1_C
  31  4ag2_D
  32  7d7s_C
  33  1azg_B
  34  1a0n_B
  35  6ipy_A
  36  1m27_C
  37  3cqt_A
  38  6ipz_Z
  39  3zl7_C
  40  1efn_C
  41  6nmw_A
  42  3ua6_A
  43  4le9_A
  44  4afu_C
  45  7a2l_B
  46  2ptk_A
  47  4k11_A
  48  1ksw_A
  49  1fmk_A
  50  6f3f_A
  51  5cdw_L
  52  4u5w_D
  53  1zbj_A
  54  7a2n_A
  55  7a2k_D
  56  3nhn_A
  57  2h8h_A
  58  1fyn_A
  59  6edf_A
  60  3h0f_A
  61  3h0i_B
  62  4d8d_A
  63  5zau_A
  64  4znx_C
  65  1x27_B
  66  7a2v_A
  67  4d8k_A
  68  1lck_A
  69  4hck_A
  70  1awx_A
  71  1qly_A
  72  7a2u_A
  73  2hck_B
  74  3vs6_A
  75  1ujy_A
  76  1kfz_A
  77  2oj2_A
  78  2sem_A
  79  1wlp_B
  80  1ov3_A
  81  2hda_A
  82  7a2p_A
  83  7a2s_A
  84  1ng2_A
  85  1uec_A
  86  1wa7_A
  87  1sem_A
  88  7a33_B
  89  7a36_A
  90  1gl5_A
  91  7a2y_A
  92  7a2w_A
  93  5sxp_B
  94  1zsg_A
  95  1uhc_A
  96  7a39_A
  97  2ega_A
  98  5nuh_D
  99  2lp5_A
  100 3rbb_B
  101 3rea_D
  102 7nes_A
  103 4cc4_F
  104 4cc2_A
  105 2ak5_A
  106 2egc_A
  107 7a3e_A
  108 4orz_A
  109 2drm_D
  110 2drk_A
  111 3reb_B
  112 6a9c_A
  113 5xg9_D
  114 7a3b_A
  115 4jz4_B
  116 7a3c_A
  117 1opl_A
  118 6amv_A
  119 1bbz_A
  120 1bbz_C
  121 1bbz_E
  122 1abo_B
  123 1abq_A
  124 4j9i_E
  125 4jjc_A
  126 4j9f_E
  127 4j9h_E
  128 4j9h_D
  129 4j9g_C
  130 4j9g_E
  131 5oaz_A
  132 4j9h_A
  133 4j9f_A
  134 4j9g_A
  135 4j9h_B
  136 4j9i_A
  137 4j9h_C
  138 4jjb_A
  139 4j9f_C
  140 5oaz_B
  141 4j9i_C
  142 5np2_A
  143 3eg1_B
  144 3eg1_A
  145 2o88_B
  146 3eg3_A
  147 4j9e_C
  148 4j9d_C
  149 4j9e_A
  150 4j9d_A
  151 4jjd_A
  152 4j9e_E
  153 4j9d_E
  154 4j9c_A
  155 5np3_B
  156 5np5_A
  157 5np3_D
  158 5np3_A
  159 5np5_B
  160 3t04_A
  161 5dc4_A
  162 3uyo_A
  163 1g83_A
  164 4xey_B
  165 3k2m_A
  166 4afz_D
  167 4afz_C
  168 4ag2_C
  169 7d7s_D
  170 1nyf_A
  171 1nyg_A
  172 1efn_A
  173 3ua7_C
  174 3ua7_A
  175 3ua7_D
  176 4eik_A
  177 3ua7_B
  178 3ua6_B
  179 4afs_C
  180 4afq_C
  181 4afu_D
  182 4afq_D
  183 7a2l_A
  184 1y57_A
  185 2src_A
  186 1cj1_J
  187 1tze_E
  188 1aze_A
  189 1gri_A
  190 5cdw_A
  191 2aoa_B
  192 1fyr_A
  193 1cj1_A
  194 5cdw_V
  195 1fhs_A
  196 3in8_A
  197 2huw_A
  198 1x0n_A
  199 1gfd_A
  200 1fyr_C
  201 1cj1_F
  202 2aoa_A
  203 3s8l_A
  204 3in7_C
  205 2vwf_A
  206 7mph_F
  207 3n8m_A
  208 1cj1_H
  209 1cj1_D
  210 5cdw_G
  211 5cdw_U
  212 5cdw_Y
  213 5cdw_K
  214 1cj1_E
  215 5cdw_d
  216 5cdw_O
  217 3n84_C
  218 5cdw_Z
  219 1io6_A
  220 7mph_B
  221 3n84_E
  222 2h46_E
  223 2aob_B
  224 3n7y_B
  225 7mph_E
  226 2aob_C
  227 1cj1_G
  228 2aob_D
  229 3imd_A
  230 6wm1_A
  231 3ove_A
  232 3n84_D
  233 3n7y_C
  234 6ich_A
  235 1fyr_B
  236 1fyr_D
  237 1zfp_E
  238 5cdw_P
  239 3n84_F
  240 5cdw_c
  241 1bm2_A
  242 6vk2_A
  243 5cdw_C
  244 3imd_B
  245 1cj1_I
  246 3wa4_A
  247 2h5k_B
  248 3mxy_A
  249 6wo2_B
  250 2huw_B
  251 4p9z_A
  252 3ov1_A
  253 1jyr_A
  254 6sdf_A
  255 3s8n_A
  256 2w0z_A
  257 7mph_C
  258 1ghu_A
  259 1jyu_A
  260 3n84_A
  261 3c7i_A
  262 3n84_B
  263 1jyq_A
  264 1gcq_B
  265 3kfj_A
  266 6icg_B
  267 1cj1_K
  268 3in7_A
  269 3s8o_A
  270 6wo2_A
  271 1cj1_C
  272 3imj_A
  273 3mxc_A
  274 4p9v_A
  275 6wm1_C
  276 5cdw_H
  277 2h5k_A
  278 1jyq_B
  279 6icg_A
  280 1bmb_A
  281 1cj1_L
  282 3n7y_A
  283 6sdf_B
  284 5cdw_E
  285 1cj1_B
  286 7mph_D
  287 1gcq_A
  288 7mph_A
  289 5cdw_B
  290 1gri_B
  291 1gfc_A
  292 2aob_A
  293 2vvk_A
  294 1qg1_E
  295 3imj_B
  296 4u5w_B
  297 1shf_B
  298 1shf_A
  299 7a2m_A
  300 7a2n_C
  301 7a2m_B
  302 7a2n_D
  303 7a2n_B
  304 7a2k_B
  305 7a2k_C
  306 7a2k_A
  307 7a2j_B
  308 7a2j_A
  309 3h0i_A
  310 3h0h_A
  311 4d8d_C
  312 1avz_C
  313 4znx_D
  314 4znx_A
  315 4znx_B
  316 1x27_D
  317 1x27_C
  318 1x27_A
  319 1x27_E
  320 1x27_F
  321 5hck_A
  322 1aww_A
  323 1ad5_A
  324 1ad5_B
  325 2hck_A
  326 5h0h_A
  327 5h0e_A
  328 3vs6_B
  329 3vs4_B
  330 3vs2_B
  331 3vs5_A
  332 2c0i_A
  333 4lud_A
  334 3vs7_A
  335 3vrz_A
  336 3vs2_A
  337 3vs3_A
  338 2c0o_A
  339 3vs1_A
  340 3vs5_B
  341 3vs1_B
  342 5h0g_A
  343 5h0b_A
  344 4lud_B
  345 4lue_B
  346 3vry_B
  347 1qcf_A
  348 2c0t_B
  349 3vs3_B
  350 5h09_A
  351 3vrz_B
  352 3vry_A
  353 2c0t_A
  354 3vs4_A
  355 4lue_A
  356 3vs7_B
  357 3vs0_B
  358 3vs0_A
  359 2c0o_B
  360 2c0i_B
  361 1k76_A
  362 2oi3_A
  363 3sem_A
  364 2sem_B
  365 3sem_B
  366 1ov3_B
  367 7a2t_A
  368 7a2q_A
  369 7a2r_A
  370 1w1f_A
  371 1sem_B
  372 7a32_B
  373 7a32_A
  374 7a31_A
  375 7a32_D
  376 7a32_C
  377 7a31_B
  378 7a33_A
  379 7a35_B
  380 7a35_A
  381 7a37_B
  382 7a37_A
  383 7a36_B
  384 7a34_A
  385 7a2z_A
  386 7a2x_A
  387 7a2o_A
  388 5sxp_C
  389 5sxp_A
  390 5sxp_D
  391 7a38_B
  392 7a39_B
  393 7a38_A
  394 7a3a_A
  395 5nuh_C
  396 2l2p_A
  397 3rbb_D
  398 3rea_B
  399 4cc4_D
  400 4cc4_B
  401 4cc7_G
  402 4cc7_C
  403 4cc7_I
  404 4cc2_C
  405 4cc3_C
  406 4cc7_E
  407 4cc7_A
  408 4cc3_E
  409 4cc3_A
  410 4cc7_M
  411 4cc3_G
  412 4cc7_K
  413 2ak5_B
  414 2drm_B
  415 2drm_A
  416 2drm_C
  417 3reb_D
  418 6a9c_B
  419 5xgg_F
  420 5xgg_C
  421 5xg9_A
  422 5xgg_A
  423 5xg9_H
  424 5xg9_B
  425 5xg9_F
  426 5xg9_G
  427 5xgg_D
  428 5xg9_C
  429 5xgg_B
  430 5xg9_E
  431 5xgg_E
  432 4rty_A
  433 4jz3_A
  434 4qt7_A
  435 4jz4_A
  436 4rtz_A
  437 7a3c_D
  438 7a3c_C
  439 7a3c_B

Test that extract hmmer works with phmmer and pdb for extract seqs using phmmer

Code
  .
Output
  # A tibble: 266 x 3
     seqs.sp      seqs.de                                seqs.dn
     <chr>        <chr>                                  <chr>  
   1 <NA>         <NA>                                   <NA>   
   2 <NA>         <NA>                                   <NA>   
   3 <NA>         <NA>                                   <NA>   
   4 <NA>         <NA>                                   <NA>   
   5 Homo sapiens proto-oncogene tyrosine-protein kinase 1opl_B 
   6 Homo sapiens Tyrosine-protein kinase ABL1           6amw_A 
   7 <NA>         <NA>                                   <NA>   
   8 Homo sapiens ABL TYROSINE KINASE                    1bbz_C 
   9 Mus musculus ABL TYROSINE KINASE                    1abo_B 
  10 Homo sapiens Tyrosine-protein kinase ABL1           4j9f_C 
  # ... with 256 more rows

Test that extract hmmer works with hmmscan and pfam for extract pdbs

Code
  .
Output
        pdbs
  1       NA
  2       NA
  3       NA
  4       NA
  5   4z4e_A
  6       NA
  7       NA
  8       NA
  9       NA
  10  4g0x_A
  11      NA
  12      NA
  13      NA
  14  5vm9_C
  15      NA
  16      NA
  17      NA
  18      NA
  19      NA
  20      NA
  21  3o3i_X
  22  1si2_A
  23      NA
  24      NA
  25  4p1z_D
  26      NA
  27  4g0o_A
  28      NA
  29      NA
  30      NA
  31      NA
  32      NA
  33      NA
  34  6oon_A
  35      NA
  36      NA
  37      NA
  38      NA
  39      NA
  40      NA
  41  7cfd_J
  42      NA
  43      NA
  44  5ygd_D
  45      NA
  46      NA
  47      NA
  48      NA
  49      NA
  50      NA
  51      NA
  52      NA
  53      NA
  54      NA
  55      NA
  56  5guh_A
  57      NA
  58      NA
  59      NA
  60      NA
  61      NA
  62      NA
  63      NA
  64  3qir_A
  65  4b9w_P
  66  4g0m_A
  67      NA
  68  7cfc_G
  69      NA
  70      NA
  71  3mj0_A
  72      NA
  73      NA
  74      NA
  75  6xup_B
  76      NA
  77      NA
  78  5g5t_A
  79      NA
  80      NA
  81      NA
  82      NA
  83      NA
  84      NA
  85      NA
  86      NA
  87      NA
  88      NA
  89      NA
  90      NA
  91      NA
  92      NA
  93      NA
  94      NA
  95      NA
  96      NA
  97      NA
  98      NA
  99      NA
  100     NA
  101     NA
  102     NA
  103     NA
  104     NA
  105     NA
  106     NA
  107     NA
  108     NA
  109     NA
  110     NA
  111 4w5t_A
  112 4z4c_A
  113 3lug_C
  114 7c6b_C
  115 6ra4_A
  116 6mfr_A
  117 5js2_A
  118 5t7b_A
  119 5js1_A
  120 3qx9_B
  121 4ola_A
  122 3luh_C
  123 4f3t_A
  124 3qx8_C
  125 7d7u_A
  126 4z4g_A
  127 3luj_C
  128 6nit_A
  129 4w5n_A
  130 6mdz_B
  131 4z4d_A
  132 4w5r_A
  133 4z4h_A
  134 3luj_A
  135 3luk_A
  136 3luc_C
  137 3qx9_C
  138 4w5q_A
  139 6mfr_B
  140 3luh_B
  141 6ra4_B
  142 3luc_B
  143 3luh_A
  144 3lud_B
  145 4z4f_A
  146 6n4o_A
  147 4olb_A
  148 3lug_A
  149 6nit_B
  150 3luc_A
  151 6mdz_A
  152 5wea_A
  153 7c6b_B
  154 3luk_B
  155 3qx8_B
  156 3luj_B
  157 4w5o_A
  158 7c6b_A
  159 7d7u_C
  160 4z4i_A
  161 3luk_C
  162 3qx8_A
  163 3lug_B
  164 7d7u_B
  165 5ki6_A
  166 3lud_C
  167 6cbd_A
  168 3qx9_A
  169 7ki3_D
  170 7ki3_A
  171 6mfn_A
  172 3lud_A
  173 3vnb_A
  174 3vna_A
  175 4g0z_A
  176 4g0p_A
  177 4g0y_A
  178 4g0q_A
  179 5vm9_A
  180 3o7v_X
  181 3o6e_X
  182 2l5c_A
  183 2l5d_A
  184 6pi7_G
  185 5w6v_A
  186 4krf_A
  187 4kre_A
  188 4kxt_A
  189 1si3_A
  190 4p1z_C
  191 4p1z_B
  192 2xfm_A
  193 4p1z_A
  194 4g0o_B
  195 3nth_C
  196 3nti_C
  197 7cfd_K
  198 7cfd_O
  199 7cfd_N
  200 7cfd_Z
  201 7cfd_M
  202 7cfd_L
  203 7cfd_I
  204 6kr6_A
  205 5ygf_D
  206 3o7x_B
  207 3qir_B
  208 3o7x_A
  209 3o7x_D
  210 3o7x_C
  211 3qir_C
  212 3qir_D
  213 4b9w_S
  214 4g0m_B
  215 7cfc_I
  216 7cfc_F
  217 7cfc_H
  218 1r6z_Z
  219 1r6z_P
  220 1t2r_A
  221 1vyn_A
  222 1r6z_A
  223 1t2s_A
  224 6xu0_B
  225 6t5t_A
  226 1w9h_A
  227 2bgg_A
  228 1ytu_A
  229 6xu0_A
  230 6tuo_A
  231 2w42_A
  232 2w42_B
  233 1ytu_B
  234 6xup_A
  235 2bgg_B
  236 5g5s_A


currocam/utilsHMMER documentation built on Feb. 19, 2023, 9:54 p.m.