Mercurial > repos > peterjc > tmhmm_and_signalp
changeset 10:09ff180d1615 draft
Uploaded v0.1.3 with missing HMM file for RXLR tool included.
| author | peterjc |
|---|---|
| date | Wed, 27 Mar 2013 11:21:05 -0400 |
| parents | e52220a9ddad |
| children | 99b82a2b1272 |
| files | tools/protein_analysis/README tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm |
| diffstat | 2 files changed, 138 insertions(+), 1 deletions(-) [+] |
line wrap: on
line diff
--- a/tools/protein_analysis/README Fri Jan 25 06:08:31 2013 -0500 +++ b/tools/protein_analysis/README Wed Mar 27 11:21:05 2013 -0400 @@ -129,6 +129,7 @@ v0.1.1 - Fixed an error in the header of the tabular output from Promoter v0.1.2 - Use the new <stdio> settings in the XML wrappers to catch errors - Use SGE style $NSLOTS for thread count (otherwise default to 4) +v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed Developers @@ -143,7 +144,7 @@ For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: -tar -czf ~/tmhmm_signalp_etc.tar.gz tools/protein_analysis/LICENSE tools/protein_analysis/README tools/protein_analysis/suite_config.xml tools/protein_analysis/seq_analysis_utils.py tools/protein_analysis/signalp3.xml tools/protein_analysis/signalp3.py tools/protein_analysis/tmhmm2.xml tools/protein_analysis/tmhmm2.py tools/protein_analysis/promoter2.xml tools/protein_analysis/promoter2.py tools/protein_analysis/wolf_psort.xml tools/protein_analysis/wolf_psort.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxlr_motifs.py test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular +tar -czf ~/tmhmm_signalp_etc.tar.gz tools/protein_analysis/LICENSE tools/protein_analysis/README tools/protein_analysis/suite_config.xml tools/protein_analysis/seq_analysis_utils.py tools/protein_analysis/signalp3.xml tools/protein_analysis/signalp3.py tools/protein_analysis/tmhmm2.xml tools/protein_analysis/tmhmm2.py tools/protein_analysis/promoter2.xml tools/protein_analysis/promoter2.py tools/protein_analysis/wolf_psort.xml tools/protein_analysis/wolf_psort.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxlr_motifs.py tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular Check this worked: @@ -162,6 +163,7 @@ tools/protein_analysis/wolf_psort.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxrl_motifs.py +tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm test-data/four_human_proteins.fasta test-data/four_human_proteins.signalp3.tabular test-data/four_human_proteins.tmhmm2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm Wed Mar 27 11:21:05 2013 -0400 @@ -0,0 +1,135 @@ +HMMER2.0 [2.3.2] +NAME cropped +LENG 39 +ALPH Amino +RF no +CS no +MAP yes +COM hmmbuild --amino consistency/cropped.hmm cropped.fas +NSEQ 39 +DATE Mon Dec 4 09:31:34 2006 +CKSUM 7487 +XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 +NULT -4 -8455 +NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 +HMM A C D E F G H I K L M N P Q R S T V W Y + m->m m->i m->d i->m i->i d->m d->d b->m m->e + -40 * -5177 + 1 -255 -3924 1452 -518 -4241 -1227 1132 -986 195 -3938 -3014 1281 153 -1634 -2181 93 1473 691 -4109 -192 5 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10298 -11340 -894 -1115 -701 -1378 -40 * + 2 764 659 1008 -569 3 -3512 1129 153 -489 -3982 -3065 808 -3605 -60 210 -327 438 1332 -4164 -3490 6 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10382 -11424 -894 -1115 -701 -1378 * * + 3 103 -4006 -696 1095 -4317 -1307 2047 -183 -1778 -483 102 1457 -786 -250 -552 562 -54 300 -4195 -3518 7 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10411 -11453 -894 -1115 -701 -1378 * * + 4 620 -4029 829 0 -576 1035 -2229 -1102 607 -4039 312 -2210 -3662 -199 -672 838 1043 -450 -4221 -425 8 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10448 -11490 -894 -1115 -701 -1378 * * + 5 -314 -4060 -780 -661 -4381 87 -2220 -1520 2552 -4076 -3149 -456 -857 1160 948 -337 -967 -378 -4243 -416 9 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10448 -11490 -894 -1115 -701 -1378 * * + 6 -8586 -7226 -8133 -8319 -8633 -7181 -7502 -9637 -7500 -8969 -8869 -8292 -7599 -7966 4272 -9023 -8672 -9332 -7346 -8510 10 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10448 -11490 -894 -1115 -701 -1378 * * + 7 -1286 -2881 -4016 -3437 2218 -4166 1024 -26 -503 1398 -2072 -897 -4230 424 -844 1397 -2725 -262 -3310 -2924 11 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10448 -11490 -894 -1115 -701 -1378 * * + 8 -7898 -6806 -8217 -8444 -5914 -7316 -7563 -5637 -8522 3411 -4888 -8458 -7570 -7966 -7946 -8843 -7894 -6444 -6753 -7295 12 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10448 -11490 -894 -1115 -701 -1378 * * + 9 -8586 -7226 -8133 -8319 -8633 -7181 -7502 -9637 -7500 -8969 -8869 -8292 -7599 -7966 4272 -9023 -8672 -9332 -7346 -8510 13 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10448 -11490 -894 -1115 -701 -1378 * * + 10 1455 -4054 -59 -793 -649 790 -2221 -4122 65 -910 -3144 332 -3656 -280 94 271 1054 265 -4239 -3558 14 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -34 -10448 -5462 -894 -1115 -701 -1378 * * + 11 113 -4029 1185 -601 -795 -271 2697 -4098 -1773 -4044 -3118 1163 -761 -266 844 -1013 74 558 -4213 664 15 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -69 -10415 -4452 -894 -1115 -1372 -704 * * + 12 151 -3974 460 544 -4295 567 1189 -4046 1955 -3990 -3063 -2110 -992 -114 56 664 -4 -3596 -4158 612 16 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -124 -10349 -3617 -894 -1115 -2170 -362 * * + 13 1133 -3868 -387 922 -4188 -1165 -2029 -919 1307 -3884 258 1329 119 -42 -2117 293 -41 -216 -4052 -3369 17 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -426 -10226 -1972 -894 -1115 -2958 -199 * * + 14 980 -3516 1162 970 -3837 -3018 822 -3587 3 -3532 -2606 781 363 -1217 1177 -1925 408 143 -3700 186 18 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -421 -9803 -1989 -894 -1115 -4103 -86 * * + 15 531 -3181 134 806 -3498 -2692 -1351 627 913 -3195 -2271 376 -2785 1432 -1440 595 -96 869 -3366 -2686 19 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -430 -9385 -1965 -894 -1115 -4592 -61 * * + 16 -1406 -2851 320 1135 -3161 -2384 -1044 187 546 420 -1944 632 -2477 901 478 140 -1345 836 -3042 -2366 20 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -667 -8960 -1441 -894 -1115 -4877 -50 * * + 17 648 -2154 -1046 1526 -2348 -2088 1765 -2027 -459 -2137 -1313 -817 -2200 -412 -922 -1045 2071 -1725 2727 -1848 21 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -158 -8299 -3314 -894 -1115 -4157 -83 * * + 18 625 -2305 823 -347 -2567 -1983 -652 329 1634 -2297 -1413 1219 -2077 -215 -756 534 -926 394 -2528 -1884 22 + - -149 -500 233 45 -381 398 105 -627 210 -466 -721 275 393 45 96 359 117 -367 -295 -244 + - -3464 -1530 -828 -60 -4628 -2975 -196 * * + 19 -2652 -4450 3714 -674 -4745 -2427 -1924 -4840 -2347 -4682 -4128 1810 -3022 -1631 -3313 -2295 -2777 -4255 -4750 -3725 24 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -9 -7966 -9008 -894 -1115 -4178 -82 * * + 20 -1035 -1481 1031 -1022 -1489 -2216 -996 -1104 -947 1100 -667 -1176 813 -825 -1297 -1229 1773 -952 -1851 1488 25 + - -149 -500 232 45 -381 398 105 -627 210 -465 -721 275 393 45 95 360 117 -365 -295 -250 + - -3313 -638 -1962 -36 -5324 -5170 -41 * * + 21 -762 -1874 -769 -248 -2169 872 -493 -1841 -93 469 -1085 1422 -1884 -89 1290 894 -720 -1508 -2203 -1616 27 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -311 -7725 -2402 -894 -1115 -4386 -71 * * + 22 -829 -1626 -1165 -895 -2419 2071 -1153 -2093 -956 318 -1475 1679 -2131 -843 -1360 1163 -968 -1683 -2602 -2084 28 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -285 -7635 -2520 -894 -1115 -4358 -72 * * + 23 740 -1215 -1188 -625 -1288 -1887 -608 1333 1229 -1100 -390 -795 -1966 1636 -769 -862 -636 852 -1606 -1144 29 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -920 -7594 -1101 -894 -1115 -1788 -493 * * + 24 -1278 -2636 1310 -622 -2911 -2270 -934 343 760 -2632 -1737 921 441 1069 -1033 -1181 1248 41 -2848 1070 30 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -5 -8765 -9807 -894 -1115 -1623 -566 * * + 25 367 -3283 2277 728 -3601 -2793 -1452 -3349 -1033 -825 -2373 280 -2886 596 188 480 -117 382 -3468 -2788 31 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -3 -9516 -10558 -894 -1115 -1352 -717 * * + 26 534 -3626 1227 1900 -3947 -3129 -1788 -601 -200 -3642 -2716 638 -480 -6 -1876 -641 1523 -875 -3810 -3128 32 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -9938 -10980 -894 -1115 -1024 -976 * * + 27 -739 -3850 1131 1319 -4171 -168 419 -3921 -1590 -3866 -2939 1855 -3444 708 276 -163 144 311 -4033 557 33 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10203 -11245 -894 -1115 -3064 -184 * * + 28 1383 -3856 786 1832 -4177 731 -2015 -3928 -365 -3872 -2946 -559 -3449 778 -2104 -657 128 215 -4040 -3357 34 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10203 -11245 -894 -1115 -725 -1340 * * + 29 692 -3936 2488 -593 -4234 -285 397 -3968 -1752 -694 -3031 -394 -908 -1709 -2256 729 -810 968 -4133 -3464 35 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10356 -11398 -894 -1115 -595 -1565 * * + 30 -1134 -4034 1957 1843 384 339 -2196 -4103 -1777 -4049 -70 831 -3631 527 -679 192 -175 -1283 -4218 -3535 36 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10420 -11462 -894 -1115 -424 -1972 * * + 31 -8459 -7269 -7060 3979 -8664 -7077 -7487 -9715 -8268 -9059 -9007 -7680 -7533 -7964 -8011 -8707 -8600 -9371 -7404 -8554 37 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10448 -11490 -894 -1115 -701 -1378 * * + 32 -5014 -7143 1163 3707 -7231 -4694 -4174 -7258 -4657 -7072 -6552 -392 -5301 -3875 -5734 -4598 -5127 -6680 -7272 -6094 38 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -10448 -11490 -894 -1115 -701 -1378 * * + 33 -5069 -5632 -5959 -4772 -6914 -5557 -3776 -6269 -2344 -5890 -5245 -4542 -5674 -259 4133 -1220 -4911 -5939 -5669 -5631 39 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -40 -10448 -5229 -894 -1115 -701 -1378 * * + 34 1552 -2931 -4 -3142 331 1758 472 -779 467 -1465 292 -3179 -4125 -2808 -713 -3061 472 386 -3346 -2943 40 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -1468 -10368 -649 -894 -1115 -371 -2142 * * + 35 846 -2494 -1545 -993 474 744 -1217 140 -893 -2442 -1628 1513 -2621 1034 384 810 -1415 -2030 -2780 842 41 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -5 -8657 -9699 -894 -1115 -93 -3998 * * + 36 -936 -2486 -4993 -4357 603 -1247 -3075 219 -3955 1137 1375 282 -842 -3580 -789 321 -678 1235 2070 1212 42 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -100 -10105 -3915 -894 -1115 -375 -2126 * * + 37 -179 -3726 -666 -266 -4047 808 447 -3798 819 -39 -2815 488 -24 140 -334 1148 730 -984 -3909 -3227 43 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -2 -9963 -11005 -894 -1115 -255 -2628 * * + 38 -839 -3715 289 -396 1009 699 -1898 1076 -234 -1572 -2806 952 841 151 521 -716 99 -945 -3903 -3225 44 + - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 + - -3 -9574 -10616 -894 -1115 -701 -1378 * * + 39 195 -2998 -1913 771 802 -2934 -1611 -2850 751 -875 683 220 -244 -1212 -1741 1189 1509 -582 -3266 -2675 45 + - * * * * * * * * * * * * * * * * * * * * + - * * * * * * * * 0 +//