From 2e038aba3dfb43822739b6f50e53ad2f9c664ab2 Mon Sep 17 00:00:00 2001 From: Danilo Horta Date: Wed, 16 Aug 2023 14:30:49 +0100 Subject: [PATCH] use local files for testing --- hmmer-reader/test/CMakeLists.txt | 46 +- hmmer-reader/test/corrupted1.hmm | 563 +++++++ hmmer-reader/test/corrupted2.hmm | 522 +++++++ hmmer-reader/test/corrupted3.hmm | 146 ++ hmmer-reader/test/corrupted4.hmm | 33 + hmmer-reader/test/corrupted5.hmm | 4 + hmmer-reader/test/corrupted6.hmm | 32 + hmmer-reader/test/corrupted7.hmm | 29 + hmmer-reader/test/corrupted8.hmm | 13 + hmmer-reader/test/empty.hmm | 0 hmmer-reader/test/three-profs.hmm | 2259 +++++++++++++++++++++++++++++ 11 files changed, 3611 insertions(+), 36 deletions(-) create mode 100644 hmmer-reader/test/corrupted1.hmm create mode 100644 hmmer-reader/test/corrupted2.hmm create mode 100644 hmmer-reader/test/corrupted3.hmm create mode 100644 hmmer-reader/test/corrupted4.hmm create mode 100644 hmmer-reader/test/corrupted5.hmm create mode 100644 hmmer-reader/test/corrupted6.hmm create mode 100644 hmmer-reader/test/corrupted7.hmm create mode 100644 hmmer-reader/test/corrupted8.hmm create mode 100644 hmmer-reader/test/empty.hmm create mode 100644 hmmer-reader/test/three-profs.hmm diff --git a/hmmer-reader/test/CMakeLists.txt b/hmmer-reader/test/CMakeLists.txt index 8d390b4..8f9ccd9 100644 --- a/hmmer-reader/test/CMakeLists.txt +++ b/hmmer-reader/test/CMakeLists.txt @@ -1,41 +1,15 @@ -function(download_files dst) - set(url "https://uk1s3.embassy.ebi.ac.uk/deciphon") - - file(DOWNLOAD ${url}/three-profs.hmm ${dst}/three-profs.hmm - EXPECTED_HASH MD5=326b9aa04c6f6213e475d5174cc3746c) - - file(DOWNLOAD ${url}/empty.hmm ${dst}/empty.hmm - EXPECTED_HASH MD5=d41d8cd98f00b204e9800998ecf8427e) - - file(DOWNLOAD ${url}/corrupted1.hmm ${dst}/corrupted1.hmm - EXPECTED_HASH MD5=df1ad566e561f92385c2d60946035eb9) - - file(DOWNLOAD ${url}/corrupted2.hmm ${dst}/corrupted2.hmm - EXPECTED_HASH MD5=c4d5cbac2aa65a76ba3dcd9bf57b7ed2) - - file(DOWNLOAD ${url}/corrupted3.hmm ${dst}/corrupted3.hmm - EXPECTED_HASH MD5=0a2b5db84ef6a5d40493226a914cde15) - - file(DOWNLOAD ${url}/corrupted4.hmm ${dst}/corrupted4.hmm - EXPECTED_HASH MD5=79730bd582b6f3ce6e1ac10946c05768) - - file(DOWNLOAD ${url}/corrupted5.hmm ${dst}/corrupted5.hmm - EXPECTED_HASH MD5=214e9f50e207150a85079c0fa2facd56) - - file(DOWNLOAD ${url}/corrupted6.hmm ${dst}/corrupted6.hmm - EXPECTED_HASH MD5=333a6b78b54c856f0ac32845901fa617) - - file(DOWNLOAD ${url}/corrupted7.hmm ${dst}/corrupted7.hmm - EXPECTED_HASH MD5=94eb1d8922400b15e2c751b370011f2c) - - file(DOWNLOAD ${url}/corrupted8.hmm ${dst}/corrupted8.hmm - EXPECTED_HASH MD5=1a17560d9c4808e0d84f95dfa41e671b) -endfunction() - set(ASSETS ${CMAKE_CURRENT_BINARY_DIR}/assets) file(MAKE_DIRECTORY ${ASSETS}) - -download_files("${ASSETS}") +file(COPY three-profs.hmm DESTINATION ${ASSETS}) +file(COPY empty.hmm DESTINATION ${ASSETS}) +file(COPY corrupted1.hmm DESTINATION ${ASSETS}) +file(COPY corrupted2.hmm DESTINATION ${ASSETS}) +file(COPY corrupted3.hmm DESTINATION ${ASSETS}) +file(COPY corrupted4.hmm DESTINATION ${ASSETS}) +file(COPY corrupted5.hmm DESTINATION ${ASSETS}) +file(COPY corrupted6.hmm DESTINATION ${ASSETS}) +file(COPY corrupted7.hmm DESTINATION ${ASSETS}) +file(COPY corrupted8.hmm DESTINATION ${ASSETS}) function(hmr_add_test name srcs) add_executable(${name} ${srcs}) diff --git a/hmmer-reader/test/corrupted1.hmm b/hmmer-reader/test/corrupted1.hmm new file mode 100644 index 0000000..758b7cf --- /dev/null +++ b/hmmer-reader/test/corrupted1.hmm @@ -0,0 +1,563 @@ +HMMER3/f [3.3.1 | Jul 2020] +NAME 1-cysPrx_C +ACC PF10417.10 +DESC C-terminal domain of 1-Cys peroxiredoxin +LENG 40 +ALPH amino +RF no +MM no +CONS yes +CS yes +MAP yes +DATE Sat Apr 18 11:53:25 2020 +NSEQ 43 +EFFN 18.158997 +CKSUM 3953450312 +GA 21.10 21.10 +TC 21.10 21.10 +NC 21.00 21.00 +STATS LOCAL MSV -7.4634 0.71948 +STATS LOCAL VITERBI -7.8384 0.71948 +STATS LOCAL FORWARD -4.3248 0.71948 +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 + COMPO 2.27455 4.34880 2.81236 2.64173 3.87711 2.69981 3.89971 3.31427 2.55515 2.85878 4.03181 3.23004 2.53005 2.90544 3.31837 2.93059 2.71936 2.60036 3.49775 3.83086 + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.00000 * + 1 0.31587 6.18340 6.83374 6.85078 7.11180 2.59795 7.26634 6.62914 6.71625 6.32654 3.30432 5.95368 5.87892 6.73911 6.62719 2.04184 4.87271 5.64306 8.45807 7.48123 1 A - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 2 4.66503 5.98593 6.64131 6.03091 1.97550 5.88281 6.17189 2.24753 5.82991 0.67731 2.90319 6.05093 6.14278 5.85183 5.79751 5.21295 4.88544 2.64552 3.19951 3.37566 2 L - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 3 4.90232 7.12275 3.75091 4.56399 6.68594 5.49209 3.78620 5.99460 2.09577 3.63808 6.18099 4.96636 5.82903 0.40174 2.57306 4.85643 5.03894 5.64288 7.30110 6.15664 3 Q - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 4 2.71456 5.31278 5.87758 3.34740 1.83324 5.10185 2.75051 3.74470 5.05317 1.60910 2.69559 5.25741 5.46573 5.18830 5.06871 4.41224 1.81592 2.33331 5.93407 2.69362 4 l - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 5 1.43762 5.73522 4.60852 4.05038 4.92778 3.02002 3.08908 4.30176 4.02260 3.99166 4.86449 3.15105 5.20200 4.34265 4.41924 2.11032 1.76717 1.69660 6.33146 3.80703 5 a - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 6 2.22519 6.30028 0.95706 1.91125 5.64394 4.56666 4.75415 5.12874 3.07402 4.60478 3.71442 4.03466 4.96047 3.36600 2.93514 3.75618 2.67384 4.69019 3.49496 5.32371 6 d - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 7 2.31663 6.30353 4.04111 1.96275 5.64947 4.56576 4.75199 5.13540 1.22906 4.60879 5.34413 4.03309 4.95911 2.62641 2.15374 2.37794 2.85742 3.79828 6.73534 3.96925 7 k - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 8 2.93970 6.30169 3.37879 1.88553 3.13321 3.50691 1.67525 5.13414 2.92075 3.46343 5.34214 2.33344 4.95608 3.06261 3.16736 2.84899 2.48750 4.69277 6.73388 2.83920 8 h - - H + 2.68633 4.42240 2.77535 2.73139 3.46369 2.40451 3.72510 3.29369 2.67632 2.69370 4.24705 2.90362 2.73755 3.18162 2.89816 2.37902 2.77535 2.98534 4.58492 3.61518 + 0.08743 2.48887 7.24920 0.07521 2.62478 0.48576 0.95510 + 9 3.91521 6.43301 3.42573 3.56093 5.78070 0.76577 4.85644 5.26795 1.94096 4.73681 5.47836 2.61355 3.30395 3.01487 3.41768 2.83024 4.14837 4.82617 6.86031 5.44689 10 g - - T + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 10 3.79868 6.20717 2.97453 1.63653 5.51188 3.50940 4.78081 2.50381 2.56438 3.06388 5.25871 3.54741 4.98139 3.89200 3.23334 2.85848 4.02990 1.20439 6.66476 5.27956 11 v - - - + 2.68633 4.42240 2.77535 2.73007 3.46369 2.40528 3.72510 3.29369 2.67756 2.69370 4.24705 2.90362 2.73755 3.17994 2.89816 2.37902 2.77535 2.98534 4.58492 3.61518 + 0.08743 2.48887 7.24920 0.07521 2.62478 0.48576 0.95510 + 11 0.93408 5.42170 3.91626 5.19935 4.54855 5.11625 5.51931 3.82501 5.04494 2.69349 4.57019 5.25883 5.51758 5.20766 5.11905 3.60399 4.24739 1.02282 6.07881 3.63869 13 a - - B + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 12 2.91228 1.25104 6.45892 5.89924 4.98288 5.65715 6.16746 2.38122 5.72170 2.84090 4.91702 5.88426 6.03314 5.87637 5.75627 5.01169 0.92001 2.82392 6.63890 5.45406 14 t - - B + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 13 7.43561 8.25050 7.76854 7.85739 8.42067 6.84623 8.42571 8.80108 8.06096 7.89736 9.20741 8.11285 0.00642 8.35756 7.83657 7.76443 7.90195 8.33235 8.76593 8.65114 15 P - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 14 0.46795 3.28176 5.43815 3.28449 5.26288 4.95835 3.49859 4.62256 4.90379 4.35312 5.24433 5.15009 5.54824 5.16412 5.17364 2.66287 4.44167 2.21901 6.72319 5.52308 16 A - - T + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 15 4.92842 7.66306 1.41254 3.95223 6.94243 1.50408 5.69272 6.51287 2.97529 5.94445 6.79889 1.10722 5.76150 2.58507 5.41405 3.74271 5.22456 6.03183 8.08159 6.50300 17 n - - T + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 16 7.92460 8.35520 7.86798 7.95582 7.48970 6.95627 8.20687 8.69962 8.10907 7.71682 9.11802 8.23318 7.58047 8.38958 7.85659 8.29931 8.29142 8.43908 0.00681 7.51434 18 W - - T + 2.68624 4.42231 2.77526 2.73129 3.46360 2.40519 3.72239 3.29360 2.67747 2.69361 4.24696 2.90353 2.73746 3.18152 2.89807 2.37893 2.77526 2.98524 4.58483 3.61509 + 0.16322 3.36269 2.15459 0.15657 1.93153 0.48576 0.95510 + 17 3.28746 6.20717 3.23713 3.01462 5.55206 3.23692 3.93035 3.26060 1.65150 4.51238 3.92232 3.07089 4.86429 2.20722 1.84764 3.29637 2.62790 2.19845 6.63997 5.22913 20 k - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00246 6.40441 7.12676 0.61958 0.77255 0.16742 1.86977 + 18 2.94743 6.32584 3.55667 2.74297 5.67283 4.58696 3.34824 3.85976 2.60710 4.62950 5.36713 4.05443 0.69153 2.59471 3.06032 3.78044 4.04904 4.71776 6.75489 5.34751 21 P - - T + 2.68930 4.42537 2.77832 2.71768 3.46019 2.40825 3.72807 3.28815 2.68053 2.69582 4.25002 2.89977 2.73738 3.17970 2.90113 2.38199 2.77181 2.98706 4.56816 3.61815 + 0.25413 1.49747 7.24920 1.97554 0.14930 0.48576 0.95510 + 19 5.25124 7.73705 4.31656 3.27102 7.24138 0.34169 5.76798 6.67396 3.55767 6.01121 6.93568 2.03219 5.98878 4.93098 3.19536 5.09902 5.50294 6.25481 8.02041 6.68204 32 G - - B + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 20 3.11421 6.32486 1.28354 1.84907 5.67093 4.57557 4.76731 5.15827 1.70938 4.63037 5.36581 4.04209 4.97263 2.85421 3.49848 2.93752 2.15646 4.71615 6.75629 5.34357 33 d - - T + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 21 3.02955 6.30262 2.13463 2.41739 5.64892 3.44892 3.37994 5.13576 1.38440 2.66263 5.34296 2.61806 2.19947 3.40789 3.47965 3.75084 3.28334 3.59967 6.73457 5.32288 34 k - - E + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 22 2.22648 3.29139 3.72055 5.15848 4.43263 2.89499 5.41983 3.77163 4.97325 2.61460 3.17921 5.20612 5.45380 5.13022 5.03022 3.37412 1.73720 1.00762 5.95781 4.77856 35 v - - E + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 23 5.72457 6.84610 7.77362 7.21618 3.03674 7.30562 7.62821 0.86870 7.13441 1.39669 1.72948 7.50659 7.14135 6.83223 7.00516 6.77102 5.91844 2.39718 7.35534 6.49761 36 i - - E + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.36660 6.52685 1.18597 0.61958 0.77255 0.48576 0.95510 + 24 3.02961 5.13404 5.74527 5.13926 3.35420 4.97012 5.32053 1.88668 4.93325 2.23086 4.25844 3.42046 2.90992 5.07072 4.94917 4.28687 4.00765 0.76706 5.80954 4.63122 37 v - - E + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.04090 6.16338 3.27098 0.61958 0.77255 2.08634 0.13255 + 25 2.76431 5.62403 4.04330 2.95922 4.85348 4.40380 4.64277 4.25151 3.48267 3.25463 4.72816 3.99026 0.80563 3.07990 3.92728 2.50151 2.94076 2.71244 6.17314 4.86715 38 p - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00325 6.12574 6.84808 0.61958 0.77255 2.15146 0.12365 + 26 2.38782 5.84711 3.37742 3.77777 5.35648 3.47549 5.01608 3.58866 3.88776 4.39740 5.22016 2.43715 0.59575 4.19537 4.34157 3.82436 4.06466 3.56212 6.65051 5.33502 39 P - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.04229 6.12574 3.23840 0.61958 0.77255 0.11061 2.25652 + 27 2.10971 6.25600 4.01591 2.79249 5.59457 4.53722 2.50840 3.62990 1.71328 4.55846 5.29841 4.00723 1.48618 3.28294 3.95334 2.54210 2.70742 4.64315 6.69255 3.81581 40 p - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00226 6.48751 7.20985 0.61958 0.77255 0.64894 0.73939 + 28 1.71056 6.24444 2.95324 3.48060 5.57357 3.66940 3.71356 3.87629 2.24126 3.21962 5.28931 3.50695 2.15313 3.26409 3.97223 2.50616 2.08990 2.36631 6.68678 5.28564 41 a - - S + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00223 6.50097 7.22331 0.61958 0.77255 0.77224 0.61985 + 29 2.90711 6.57118 2.08714 3.26144 5.94405 4.72182 5.01961 5.43771 3.36825 4.91551 5.66922 4.20473 2.97205 4.13119 4.32553 1.31040 1.08628 4.99057 7.04983 5.62125 42 t - - S + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00223 6.50097 7.22331 0.61958 0.77255 0.77224 0.61985 + 30 3.14042 4.07690 2.69202 2.01472 3.42438 4.55921 3.95463 3.71711 3.49557 3.76435 5.26582 3.25429 2.17379 2.02796 3.50770 2.75342 2.92220 2.81633 6.66726 2.29323 43 e - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00223 6.50097 7.22331 0.61958 0.77255 0.34098 1.24158 + 31 3.82920 6.34689 1.53105 1.18752 5.69212 3.68922 3.28922 5.18035 2.08868 4.65220 5.38846 2.78144 4.98834 2.53646 4.02124 3.78845 3.59068 3.72431 6.77837 5.36379 44 e - 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- C + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00147 6.52614 * 0.61958 0.77255 0.00000 * +// +HMMER3/f [3.3.1 | Jul 2020] +NAME 17kDa_Anti_2 +ACC PF16998.6 +DESC 17 kDa outer membrane surface antigen +LENG 116 +ALPH amino +RF no +MM no +CONS yes +CS no +MAP yes +DATE Thu Apr 23 07:14:02 2020 +NSEQ 7 +EFFN 0.967285 +CKSUM 526719753 +GA 26.60 26.60 +TC 26.60 26.60 +NC 26.40 26.50 +STATS LOCAL MSV -9.7261 0.71424 +STATS LOCAL VITERBI -10.6405 0.71424 +STATS LOCAL FORWARD -4.3812 0.71424 +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 + COMPO 2.44156 3.92893 2.87357 2.68018 3.52118 2.58424 3.87247 2.99320 2.72722 2.78029 3.84043 3.03445 3.39718 3.05202 2.91140 2.46260 2.62228 2.72871 4.09756 3.89187 + 2.68621 4.42228 2.77523 2.73127 3.46357 2.40490 3.72498 3.29357 2.67744 2.69358 4.24693 2.90350 2.73743 3.18150 2.89804 2.37877 2.77523 2.98522 4.58480 3.61506 + 0.62813 1.53465 1.38277 0.22956 1.58416 0.00000 * + 1 2.69007 4.46370 3.36806 3.26995 4.41231 0.69816 4.38917 4.01673 3.45404 3.66834 4.64409 3.53231 3.85550 3.77654 3.68802 2.86253 3.17289 3.54108 5.50224 4.51483 2 g - 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- - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.09167 4.17189 2.62874 0.61958 0.77255 0.48576 0.95510 + 116 2.35737 4.32302 3.51836 2.95621 3.38530 3.58989 3.83198 2.39981 2.83615 2.47713 3.41024 3.34439 3.97440 2.50125 3.15837 2.85178 2.85508 2.57784 2.75537 3.59346 122 a - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01676 4.09698 * 0.61958 0.77255 0.00000 * +// +HMMER3/f [3.3.1 | Jul 2020] +NAME 2-ph_phosp +ACC PF04029.15 +DESC 2-phosphosulpholactate phosphatase +LENG 226 +ALPH amino +RF no +MM no +CONS yes +CS yes +MAP yes +DATE Thu Apr 16 23:33:24 2020 +NSEQ 131 +EFFN 3.010345 +CKSUM 1129448243 +GA 26.40 26.40 +TC 26.50 26.50 +NC 25.90 25.20 +STATS LOCAL MSV -10.5421 0.70394 +STATS LOCAL VITERBI -11.3818 0.70394 +STATS LOCAL FORWARD -5.3991 0.70394 +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 + COMPO 2.35591 4.12427 2.90855 2.64100 3.47008 2.87269 3.83727 2.77543 2.76578 2.38722 3.72809 3.03236 3.54966 3.13439 3.02110 2.65983 2.74200 2.54712 5.06064 3.70798 + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.40383 4.92963 1.12388 0.61958 0.77255 0.00000 * + 1 2.54942 3.03891 3.20230 3.50074 2.88555 3.81717 3.93610 2.22407 3.50689 2.12701 3.28287 3.45293 4.18593 3.71739 3.66849 3.06889 2.87718 2.20595 3.86411 2.52117 1 l - - C + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01596 4.54176 5.26410 0.61958 0.77255 0.79974 0.59683 + 2 2.65659 4.72879 2.86429 2.53282 2.99174 3.58038 2.81194 3.00942 2.73345 1.98800 3.72713 3.03839 3.53875 3.06834 3.00952 2.73733 2.97927 2.95574 5.27164 3.66928 2 l - - C + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01423 4.65509 5.37743 0.61958 0.77255 0.78334 0.61042 + 3 2.61893 4.48713 3.66748 3.09928 3.62360 3.75738 4.01237 2.08153 2.89695 2.42620 3.59151 3.50062 3.81684 3.35097 2.75400 2.57217 1.89259 2.61642 5.07086 3.73087 3 t - - S + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01336 4.71812 5.44046 0.61958 0.77255 0.74195 0.64662 + 4 2.59006 4.84488 3.29402 2.52840 4.04601 3.65835 3.74680 3.32321 2.37545 2.91317 3.92758 3.18609 1.73520 3.06055 3.15438 2.80966 3.02365 2.51439 5.37464 3.54942 4 p - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01276 4.76385 5.48620 0.61958 0.77255 0.76786 0.62363 + 5 2.53384 4.98866 2.26961 1.70948 4.64561 3.29332 3.33306 4.13093 2.25245 3.60657 4.34314 2.74126 3.95969 2.51796 2.91080 2.61246 3.02484 3.64225 5.73520 4.14807 5 e - - C + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01256 4.77948 5.50183 0.61958 0.77255 0.61703 0.77554 diff --git a/hmmer-reader/test/corrupted2.hmm b/hmmer-reader/test/corrupted2.hmm new file mode 100644 index 0000000..d64e344 --- /dev/null +++ b/hmmer-reader/test/corrupted2.hmm @@ -0,0 +1,522 @@ +HMMER3/f [3.3.1 | Jul 2020] +NAME 1-cysPrx_C +ACC PF10417.10 +DESC C-terminal domain of 1-Cys peroxiredoxin +LENG 40 +ALPH amino +RF no +MM no +CONS yes +CS yes +MAP yes +DATE Sat Apr 18 11:53:25 2020 +NSEQ 43 +EFFN 18.158997 +CKSUM 3953450312 +GA 21.10 21.10 +TC 21.10 21.10 +NC 21.00 21.00 +STATS LOCAL MSV -7.4634 0.71948 +STATS LOCAL VITERBI -7.8384 0.71948 +STATS LOCAL FORWARD -4.3248 0.71948 +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 + COMPO 2.27455 4.34880 2.81236 2.64173 3.87711 2.69981 3.89971 3.31427 2.55515 2.85878 4.03181 3.23004 2.53005 2.90544 3.31837 2.93059 2.71936 2.60036 3.49775 3.83086 + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.00000 * + 1 0.31587 6.18340 6.83374 6.85078 7.11180 2.59795 7.26634 6.62914 6.71625 6.32654 3.30432 5.95368 5.87892 6.73911 6.62719 2.04184 4.87271 5.64306 8.45807 7.48123 1 A - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 2 4.66503 5.98593 6.64131 6.03091 1.97550 5.88281 6.17189 2.24753 5.82991 0.67731 2.90319 6.05093 6.14278 5.85183 5.79751 5.21295 4.88544 2.64552 3.19951 3.37566 2 L - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 3 4.90232 7.12275 3.75091 4.56399 6.68594 5.49209 3.78620 5.99460 2.09577 3.63808 6.18099 4.96636 5.82903 0.40174 2.57306 4.85643 5.03894 5.64288 7.30110 6.15664 3 Q - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 4 2.71456 5.31278 5.87758 3.34740 1.83324 5.10185 2.75051 3.74470 5.05317 1.60910 2.69559 5.25741 5.46573 5.18830 5.06871 4.41224 1.81592 2.33331 5.93407 2.69362 4 l - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 5 1.43762 5.73522 4.60852 4.05038 4.92778 3.02002 3.08908 4.30176 4.02260 3.99166 4.86449 3.15105 5.20200 4.34265 4.41924 2.11032 1.76717 1.69660 6.33146 3.80703 5 a - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 6 2.22519 6.30028 0.95706 1.91125 5.64394 4.56666 4.75415 5.12874 3.07402 4.60478 3.71442 4.03466 4.96047 3.36600 2.93514 3.75618 2.67384 4.69019 3.49496 5.32371 6 d - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 7 2.31663 6.30353 4.04111 1.96275 5.64947 4.56576 4.75199 5.13540 1.22906 4.60879 5.34413 4.03309 4.95911 2.62641 2.15374 2.37794 2.85742 3.79828 6.73534 3.96925 7 k - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 8 2.93970 6.30169 3.37879 1.88553 3.13321 3.50691 1.67525 5.13414 2.92075 3.46343 5.34214 2.33344 4.95608 3.06261 3.16736 2.84899 2.48750 4.69277 6.73388 2.83920 8 h - - H + 2.68633 4.42240 2.77535 2.73139 3.46369 2.40451 3.72510 3.29369 2.67632 2.69370 4.24705 2.90362 2.73755 3.18162 2.89816 2.37902 2.77535 2.98534 4.58492 3.61518 + 0.08743 2.48887 7.24920 0.07521 2.62478 0.48576 0.95510 + 9 3.91521 6.43301 3.42573 3.56093 5.78070 0.76577 4.85644 5.26795 1.94096 4.73681 5.47836 2.61355 3.30395 3.01487 3.41768 2.83024 4.14837 4.82617 6.86031 5.44689 10 g - - T + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 10 3.79868 6.20717 2.97453 1.63653 5.51188 3.50940 4.78081 2.50381 2.56438 3.06388 5.25871 3.54741 4.98139 3.89200 3.23334 2.85848 4.02990 1.20439 6.66476 5.27956 11 v - - - + 2.68633 4.42240 2.77535 2.73007 3.46369 2.40528 3.72510 3.29369 2.67756 2.69370 4.24705 2.90362 2.73755 3.17994 2.89816 2.37902 2.77535 2.98534 4.58492 3.61518 + 0.08743 2.48887 7.24920 0.07521 2.62478 0.48576 0.95510 + 11 0.93408 5.42170 3.91626 5.19935 4.54855 5.11625 5.51931 3.82501 5.04494 2.69349 4.57019 5.25883 5.51758 5.20766 5.11905 3.60399 4.24739 1.02282 6.07881 3.63869 13 a - - B + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 12 2.91228 1.25104 6.45892 5.89924 4.98288 5.65715 6.16746 2.38122 5.72170 2.84090 4.91702 5.88426 6.03314 5.87637 5.75627 5.01169 0.92001 2.82392 6.63890 5.45406 14 t - - B + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 13 7.43561 8.25050 7.76854 7.85739 8.42067 6.84623 8.42571 8.80108 8.06096 7.89736 9.20741 8.11285 0.00642 8.35756 7.83657 7.76443 7.90195 8.33235 8.76593 8.65114 15 P - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 14 0.46795 3.28176 5.43815 3.28449 5.26288 4.95835 3.49859 4.62256 4.90379 4.35312 5.24433 5.15009 5.54824 5.16412 5.17364 2.66287 4.44167 2.21901 6.72319 5.52308 16 A - - T + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 15 4.92842 7.66306 1.41254 3.95223 6.94243 1.50408 5.69272 6.51287 2.97529 5.94445 6.79889 1.10722 5.76150 2.58507 5.41405 3.74271 5.22456 6.03183 8.08159 6.50300 17 n - - T + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 16 7.92460 8.35520 7.86798 7.95582 7.48970 6.95627 8.20687 8.69962 8.10907 7.71682 9.11802 8.23318 7.58047 8.38958 7.85659 8.29931 8.29142 8.43908 0.00681 7.51434 18 W - - T + 2.68624 4.42231 2.77526 2.73129 3.46360 2.40519 3.72239 3.29360 2.67747 2.69361 4.24696 2.90353 2.73746 3.18152 2.89807 2.37893 2.77526 2.98524 4.58483 3.61509 + 0.16322 3.36269 2.15459 0.15657 1.93153 0.48576 0.95510 + 17 3.28746 6.20717 3.23713 3.01462 5.55206 3.23692 3.93035 3.26060 1.65150 4.51238 3.92232 3.07089 4.86429 2.20722 1.84764 3.29637 2.62790 2.19845 6.63997 5.22913 20 k - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00246 6.40441 7.12676 0.61958 0.77255 0.16742 1.86977 + 18 2.94743 6.32584 3.55667 2.74297 5.67283 4.58696 3.34824 3.85976 2.60710 4.62950 5.36713 4.05443 0.69153 2.59471 3.06032 3.78044 4.04904 4.71776 6.75489 5.34751 21 P - - T + 2.68930 4.42537 2.77832 2.71768 3.46019 2.40825 3.72807 3.28815 2.68053 2.69582 4.25002 2.89977 2.73738 3.17970 2.90113 2.38199 2.77181 2.98706 4.56816 3.61815 + 0.25413 1.49747 7.24920 1.97554 0.14930 0.48576 0.95510 + 19 5.25124 7.73705 4.31656 3.27102 7.24138 0.34169 5.76798 6.67396 3.55767 6.01121 6.93568 2.03219 5.98878 4.93098 3.19536 5.09902 5.50294 6.25481 8.02041 6.68204 32 G - - B + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 20 3.11421 6.32486 1.28354 1.84907 5.67093 4.57557 4.76731 5.15827 1.70938 4.63037 5.36581 4.04209 4.97263 2.85421 3.49848 2.93752 2.15646 4.71615 6.75629 5.34357 33 d - - T + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 21 3.02955 6.30262 2.13463 2.41739 5.64892 3.44892 3.37994 5.13576 1.38440 2.66263 5.34296 2.61806 2.19947 3.40789 3.47965 3.75084 3.28334 3.59967 6.73457 5.32288 34 k - - E + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 22 2.22648 3.29139 3.72055 5.15848 4.43263 2.89499 5.41983 3.77163 4.97325 2.61460 3.17921 5.20612 5.45380 5.13022 5.03022 3.37412 1.73720 1.00762 5.95781 4.77856 35 v - 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- C + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00147 6.52614 * 0.61958 0.77255 0.00000 * +// +HMMER3/f [3.3.1 | Jul 2020] +NAME 17kDa_Anti_2 +ACC PF16998.6 +DESC 17 kDa outer membrane surface antigen +LENG 116 +ALPHamino +RF no +MM no +CONS yes +CS no +MAP yes +DATE Thu Apr 23 07:14:02 2020 +NSEQ 7 +EFFN 0.967285 +CKSUM 526719753 +GA 26.60 26.60 +TC 26.60 26.60 +NC 26.40 26.50 +STATS LOCAL MSV -9.7261 0.71424 +STATS LOCAL VITERBI -10.6405 0.71424 +STATS LOCAL FORWARD -4.3812 0.71424 +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 + COMPO 2.44156 3.92893 2.87357 2.68018 3.52118 2.58424 3.87247 2.99320 2.72722 2.78029 3.84043 3.03445 3.39718 3.05202 2.91140 2.46260 2.62228 2.72871 4.09756 3.89187 + 2.68621 4.42228 2.77523 2.73127 3.46357 2.40490 3.72498 3.29357 2.67744 2.69358 4.24693 2.90350 2.73743 3.18150 2.89804 2.37877 2.77523 2.98522 4.58480 3.61506 + 0.62813 1.53465 1.38277 0.22956 1.58416 0.00000 * + 1 2.69007 4.46370 3.36806 3.26995 4.41231 0.69816 4.38917 4.01673 3.45404 3.66834 4.64409 3.53231 3.85550 3.77654 3.68802 2.86253 3.17289 3.54108 5.50224 4.51483 2 g - 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- - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02318 4.17189 4.89423 0.61958 0.77255 0.48576 0.95510 + 110 3.28306 4.56561 5.04862 4.50657 3.37024 4.65176 5.07543 1.46803 4.38727 1.20939 3.15554 4.71899 4.86502 4.53014 4.51230 4.01810 3.52054 1.62569 5.41513 4.30784 116 l - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02318 4.17189 4.89423 0.61958 0.77255 0.48576 0.95510 + 111 2.63938 4.60552 3.22229 2.65573 3.80319 3.51330 3.72645 3.16498 2.53184 2.53656 3.69933 3.12727 3.90338 2.53595 2.53684 2.74831 2.13330 2.58543 5.15009 3.87538 117 t - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02318 4.17189 4.89423 0.61958 0.77255 0.48576 0.95510 + 112 2.01699 4.45674 3.23063 2.82670 4.27451 3.17272 3.99508 3.68955 2.87558 3.33261 4.14868 2.58109 3.80316 3.19554 3.27993 1.54633 2.27077 3.23665 5.57295 4.29657 118 s - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02318 4.17189 4.89423 0.61958 0.77255 0.48576 0.95510 + 113 3.46053 4.77661 4.86708 4.40451 1.30169 4.53140 4.30082 2.51766 4.24735 1.27692 3.14574 4.46961 4.77805 4.30825 4.32236 3.90847 3.69002 2.63013 4.49656 2.95417 119 l - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02318 4.17189 4.89423 0.61958 0.77255 0.48576 0.95510 + 114 2.34679 5.07617 2.55712 2.34075 4.39571 2.70953 3.60781 3.85679 2.11622 3.36828 4.13403 2.88262 3.80974 2.46745 2.48324 2.62594 2.88407 3.45518 5.52542 4.13899 120 k - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02318 4.17189 4.89423 0.61958 0.77255 0.48576 0.95510 + 115 2.83129 5.03378 2.90659 2.53451 4.39570 3.47097 3.73503 3.81822 2.08323 3.36473 4.20655 3.03286 1.70001 2.46935 2.69201 2.83924 3.07775 3.47265 5.53380 4.22868 121 p - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.09167 4.17189 2.62874 0.61958 0.77255 0.48576 0.95510 + 116 2.35737 4.32302 3.51836 2.95621 3.38530 3.58989 3.83198 2.39981 2.83615 2.47713 3.41024 3.34439 3.97440 2.50125 3.15837 2.85178 2.85508 2.57784 2.75537 3.59346 122 a - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.01676 4.09698 * 0.61958 0.77255 0.00000 * +// diff --git a/hmmer-reader/test/corrupted3.hmm b/hmmer-reader/test/corrupted3.hmm new file mode 100644 index 0000000..8e70c61 --- /dev/null +++ b/hmmer-reader/test/corrupted3.hmm @@ -0,0 +1,146 @@ +HMMER3/f [3.3.1 | Jul 2020] +NAME 1-cysPrx_C +ACC PF10417.10 +DESC C-terminal domain of 1-Cys peroxiredoxin +ALPH amino +RF no +MM no +CONS yes +CS yes +MAP yes +DATE Sat Apr 18 11:53:25 2020 +NSEQ 43 +EFFN 18.158997 +CKSUM 3953450312 +GA 21.10 21.10 +TC 21.10 21.10 +NC 21.00 21.00 +STATS LOCAL MSV -7.4634 0.71948 +STATS LOCAL VITERBI -7.8384 0.71948 +STATS LOCAL FORWARD -4.3248 0.71948 +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 + COMPO 2.27455 4.34880 2.81236 2.64173 3.87711 2.69981 3.89971 3.31427 2.55515 2.85878 4.03181 3.23004 2.53005 2.90544 3.31837 2.93059 2.71936 2.60036 3.49775 3.83086 + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.00000 * + 1 0.31587 6.18340 6.83374 6.85078 7.11180 2.59795 7.26634 6.62914 6.71625 6.32654 3.30432 5.95368 5.87892 6.73911 6.62719 2.04184 4.87271 5.64306 8.45807 7.48123 1 A - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 2 4.66503 5.98593 6.64131 6.03091 1.97550 5.88281 6.17189 2.24753 5.82991 0.67731 2.90319 6.05093 6.14278 5.85183 5.79751 5.21295 4.88544 2.64552 3.19951 3.37566 2 L - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 3 4.90232 7.12275 3.75091 4.56399 6.68594 5.49209 3.78620 5.99460 2.09577 3.63808 6.18099 4.96636 5.82903 0.40174 2.57306 4.85643 5.03894 5.64288 7.30110 6.15664 3 Q - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 4 2.71456 5.31278 5.87758 3.34740 1.83324 5.10185 2.75051 3.74470 5.05317 1.60910 2.69559 5.25741 5.46573 5.18830 5.06871 4.41224 1.81592 2.33331 5.93407 2.69362 4 l - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 5 1.43762 5.73522 4.60852 4.05038 4.92778 3.02002 3.08908 4.30176 4.02260 3.99166 4.86449 3.15105 5.20200 4.34265 4.41924 2.11032 1.76717 1.69660 6.33146 3.80703 5 a - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 6 2.22519 6.30028 0.95706 1.91125 5.64394 4.56666 4.75415 5.12874 3.07402 4.60478 3.71442 4.03466 4.96047 3.36600 2.93514 3.75618 2.67384 4.69019 3.49496 5.32371 6 d - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 7 2.31663 6.30353 4.04111 1.96275 5.64947 4.56576 4.75199 5.13540 1.22906 4.60879 5.34413 4.03309 4.95911 2.62641 2.15374 2.37794 2.85742 3.79828 6.73534 3.96925 7 k - 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- - + 2.68633 4.42240 2.77535 2.73007 3.46369 2.40528 3.72510 3.29369 2.67756 2.69370 4.24705 2.90362 2.73755 3.17994 2.89816 2.37902 2.77535 2.98534 4.58492 3.61518 + 0.08743 2.48887 7.24920 0.07521 2.62478 0.48576 0.95510 + 11 0.93408 5.42170 3.91626 5.19935 4.54855 5.11625 5.51931 3.82501 5.04494 2.69349 4.57019 5.25883 5.51758 5.20766 5.11905 3.60399 4.24739 1.02282 6.07881 3.63869 13 a - - B + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 12 2.91228 1.25104 6.45892 5.89924 4.98288 5.65715 6.16746 2.38122 5.72170 2.84090 4.91702 5.88426 6.03314 5.87637 5.75627 5.01169 0.92001 2.82392 6.63890 5.45406 14 t - - B + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 13 7.43561 8.25050 7.76854 7.85739 8.42067 6.84623 8.42571 8.80108 8.06096 7.89736 9.20741 8.11285 0.00642 8.35756 7.83657 7.76443 7.90195 8.33235 8.76593 8.65114 15 P - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 14 0.46795 3.28176 5.43815 3.28449 5.26288 4.95835 3.49859 4.62256 4.90379 4.35312 5.24433 5.15009 5.54824 5.16412 5.17364 2.66287 4.44167 2.21901 6.72319 5.52308 16 A - - T + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 15 4.92842 7.66306 1.41254 3.95223 6.94243 1.50408 5.69272 6.51287 2.97529 5.94445 6.79889 1.10722 5.76150 2.58507 5.41405 3.74271 5.22456 6.03183 8.08159 6.50300 17 n - - T + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 16 7.92460 8.35520 7.86798 7.95582 7.48970 6.95627 8.20687 8.69962 8.10907 7.71682 9.11802 8.23318 7.58047 8.38958 7.85659 8.29931 8.29142 8.43908 0.00681 7.51434 18 W - - T + 2.68624 4.42231 2.77526 2.73129 3.46360 2.40519 3.72239 3.29360 2.67747 2.69361 4.24696 2.90353 2.73746 3.18152 2.89807 2.37893 2.77526 2.98524 4.58483 3.61509 + 0.16322 3.36269 2.15459 0.15657 1.93153 0.48576 0.95510 + 17 3.28746 6.20717 3.23713 3.01462 5.55206 3.23692 3.93035 3.26060 1.65150 4.51238 3.92232 3.07089 4.86429 2.20722 1.84764 3.29637 2.62790 2.19845 6.63997 5.22913 20 k - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00246 6.40441 7.12676 0.61958 0.77255 0.16742 1.86977 + 18 2.94743 6.32584 3.55667 2.74297 5.67283 4.58696 3.34824 3.85976 2.60710 4.62950 5.36713 4.05443 0.69153 2.59471 3.06032 3.78044 4.04904 4.71776 6.75489 5.34751 21 P - - T + 2.68930 4.42537 2.77832 2.71768 3.46019 2.40825 3.72807 3.28815 2.68053 2.69582 4.25002 2.89977 2.73738 3.17970 2.90113 2.38199 2.77181 2.98706 4.56816 3.61815 + 0.25413 1.49747 7.24920 1.97554 0.14930 0.48576 0.95510 + 19 5.25124 7.73705 4.31656 3.27102 7.24138 0.34169 5.76798 6.67396 3.55767 6.01121 6.93568 2.03219 5.98878 4.93098 3.19536 5.09902 5.50294 6.25481 8.02041 6.68204 32 G - - B + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 20 3.11421 6.32486 1.28354 1.84907 5.67093 4.57557 4.76731 5.15827 1.70938 4.63037 5.36581 4.04209 4.97263 2.85421 3.49848 2.93752 2.15646 4.71615 6.75629 5.34357 33 d - - T + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 21 3.02955 6.30262 2.13463 2.41739 5.64892 3.44892 3.37994 5.13576 1.38440 2.66263 5.34296 2.61806 2.19947 3.40789 3.47965 3.75084 3.28334 3.59967 6.73457 5.32288 34 k - - E + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 22 2.22648 3.29139 3.72055 5.15848 4.43263 2.89499 5.41983 3.77163 4.97325 2.61460 3.17921 5.20612 5.45380 5.13022 5.03022 3.37412 1.73720 1.00762 5.95781 4.77856 35 v - - E + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 23 5.72457 6.84610 7.77362 7.21618 3.03674 7.30562 7.62821 0.86870 7.13441 1.39669 1.72948 7.50659 7.14135 6.83223 7.00516 6.77102 5.91844 2.39718 7.35534 6.49761 36 i - - E + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.36660 6.52685 1.18597 0.61958 0.77255 0.48576 0.95510 + 24 3.02961 5.13404 5.74527 5.13926 3.35420 4.97012 5.32053 1.88668 4.93325 2.23086 4.25844 3.42046 2.90992 5.07072 4.94917 4.28687 4.00765 0.76706 5.80954 4.63122 37 v - - E + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.04090 6.16338 3.27098 0.61958 0.77255 2.08634 0.13255 + 25 2.76431 5.62403 4.04330 2.95922 4.85348 4.40380 4.64277 4.25151 3.48267 3.25463 4.72816 3.99026 0.80563 3.07990 3.92728 2.50151 2.94076 2.71244 6.17314 4.86715 38 p - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00325 6.12574 6.84808 0.61958 0.77255 2.15146 0.12365 + 26 2.38782 5.84711 3.37742 3.77777 5.35648 3.47549 5.01608 3.58866 3.88776 4.39740 5.22016 2.43715 0.59575 4.19537 4.34157 3.82436 4.06466 3.56212 6.65051 5.33502 39 P - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.04229 6.12574 3.23840 0.61958 0.77255 0.11061 2.25652 + 27 2.10971 6.25600 4.01591 2.79249 5.59457 4.53722 2.50840 3.62990 1.71328 4.55846 5.29841 4.00723 1.48618 3.28294 3.95334 2.54210 2.70742 4.64315 6.69255 3.81581 40 p - - - + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00226 6.48751 7.20985 0.61958 0.77255 0.64894 0.73939 + 28 1.71056 6.24444 2.95324 3.48060 5.57357 3.66940 3.71356 3.87629 2.24126 3.21962 5.28931 3.50695 2.15313 3.26409 3.97223 2.50616 2.08990 2.36631 6.68678 5.28564 41 a - - S + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00223 6.50097 7.22331 0.61958 0.77255 0.77224 0.61985 + 29 2.90711 6.57118 2.08714 3.26144 5.94405 4.72182 5.01961 5.43771 3.36825 4.91551 5.66922 4.20473 2.97205 4.13119 4.32553 1.31040 1.08628 4.99057 7.04983 5.62125 42 t - - S + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00223 6.50097 7.22331 0.61958 0.77255 0.77224 0.61985 + 30 3.14042 4.07690 2.69202 2.01472 3.42438 4.55921 3.95463 3.71711 3.49557 3.76435 5.26582 3.25429 2.17379 2.02796 3.50770 2.75342 2.92220 2.81633 6.66726 2.29323 43 e - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00223 6.50097 7.22331 0.61958 0.77255 0.34098 1.24158 + 31 3.82920 6.34689 1.53105 1.18752 5.69212 3.68922 3.28922 5.18035 2.08868 4.65220 5.38846 2.78144 4.98834 2.53646 4.02124 3.78845 3.59068 3.72431 6.77837 5.36379 44 e - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.36342 6.52685 1.19322 0.61958 0.77255 0.48576 0.95510 + 32 2.87588 6.03057 1.33540 1.63222 5.37232 3.39598 4.48989 4.85601 3.22604 2.84850 2.77535 3.77084 4.69578 2.62540 3.06267 2.95892 3.16130 4.41944 6.46523 5.05619 45 d - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.04057 6.16656 3.27922 0.61958 0.77255 0.21762 1.63185 + 33 0.92006 5.36478 5.33147 4.74963 4.48620 2.00523 5.29585 2.65751 3.43910 3.18437 4.49566 4.95604 5.34451 4.85600 4.81924 2.62280 2.90416 2.19046 5.99279 4.80047 46 a - - H + 2.68652 4.42259 2.77553 2.73157 3.46388 2.40359 3.72528 3.29388 2.67650 2.69389 4.24723 2.90380 2.73773 3.18180 2.89682 2.37920 2.77553 2.98552 4.58511 3.61537 + 0.10333 2.32883 7.17647 0.68718 0.69915 0.47004 0.98077 + 34 3.11404 6.08924 4.13030 2.62888 5.35759 4.59739 4.79473 2.07408 2.10796 2.91485 5.15101 3.63348 4.98851 2.79738 2.68182 2.39632 3.48644 1.41188 6.57073 5.21169 49 v - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00223 6.50097 7.22331 0.61958 0.77255 0.34098 1.24158 + 35 2.28816 4.04483 3.00729 2.07918 5.64904 3.11863 4.74932 5.13591 1.12307 4.60852 5.34303 3.23013 4.95589 2.45290 3.50015 3.02818 3.13708 4.69402 3.33548 5.32291 50 k - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 36 3.24275 4.21091 2.48056 1.65898 5.64895 3.83849 3.71569 5.13578 2.28239 3.79751 3.97460 3.08413 4.95593 3.11107 1.20406 3.75085 3.28334 4.69394 6.73457 5.32289 51 r - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 37 3.29213 5.31256 5.87840 3.50495 2.25522 5.10186 5.43436 3.31225 5.05370 1.61705 2.80705 5.25773 5.46574 3.62909 3.96662 4.41229 3.35090 2.58147 5.93399 1.11578 52 y - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02799 6.52685 3.64430 0.61958 0.77255 0.48576 0.95510 + 38 3.78361 3.91484 3.48009 2.47310 2.34448 3.30813 4.78319 3.15524 2.34947 1.92789 5.17732 4.08707 2.64826 2.14857 3.50509 2.89223 3.12036 4.47323 2.78785 5.22592 53 l - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00223 6.50109 7.22344 0.61958 0.77255 0.77102 0.62090 + 39 2.86294 6.29310 2.70442 1.35947 5.63929 2.63349 4.73760 5.12653 2.17285 4.59887 5.33369 2.67516 4.94342 2.67610 3.96687 2.09465 2.34079 4.68438 6.72490 5.31247 54 e - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00223 6.50109 7.22344 0.61958 0.77255 0.34148 1.24036 + 40 3.24278 6.30083 3.43353 3.14617 5.64633 1.15426 3.96934 5.13260 1.91225 3.12877 5.34138 2.52728 4.95630 3.00879 3.59455 2.76944 2.63230 3.85185 6.73327 3.76690 55 g - - C + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00147 6.52614 * 0.61958 0.77255 0.00000 * +// diff --git a/hmmer-reader/test/corrupted4.hmm b/hmmer-reader/test/corrupted4.hmm new file mode 100644 index 0000000..4db8e44 --- /dev/null +++ b/hmmer-reader/test/corrupted4.hmm @@ -0,0 +1,33 @@ +HMMER3/f [3.3.1 | Jul 2020] +NAME 1-cysPrx_C +ACC PF10417.10 +DESC C-terminal domain of 1-Cys peroxiredoxin +LENG 40 +ALPH amino +RF no +MM no +CONS yes +CS yes +MAP yes +DATE Sat Apr 18 11:53:25 2020 +NSEQ 43 +EFFN 18.158997 +CKSUM 3953450312 +GA 21.10 21.10 +TC 21.10 21.10 +NC 21.00 21.00 +STATS LOCAL MSV -7.4634 0.71948 +STATS LOCAL VITERBI -7.8384 0.71948 +STATS LOCAL FORWARD -4.3248 0.71948 +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 + COMPO 2.27455 4.34880 2.81236 2.64173 3.87711 2.69981 3.89971 3.31427 2.55515 2.85878 4.03181 3.23004 2.53005 2.90544 3.31837 2.93059 2.71936 2.60036 3.49775 3.83086 + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.00000 * + 1 0.31587 6.18340 6.83374 6.85078 7.11180 2.59795 7.26634 6.62914 6.71625 6.32654 3.30432 5.95368 5.87892 6.73911 6.62719 2.04184 4.87271 5.64306 8.45807 7.48123 1 A - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 2 4.66503 5.98593 6.64131 6.03091 1.97550 5.88281 6.17189 2.24753 5.82991 0.67731 2.90319 6.05093 6.14278 5.85183 5.79751 5.21295 4.88544 2.64552 3.19951 3.37566 2 L - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 +// diff --git a/hmmer-reader/test/corrupted5.hmm b/hmmer-reader/test/corrupted5.hmm new file mode 100644 index 0000000..8d696bc --- /dev/null +++ b/hmmer-reader/test/corrupted5.hmm @@ -0,0 +1,4 @@ +HMMER3/f [3.3.1 | Jul 2020] +NAME 1-cysPrx_C +ACC PF10417.10 +// diff --git a/hmmer-reader/test/corrupted6.hmm b/hmmer-reader/test/corrupted6.hmm new file mode 100644 index 0000000..22138d3 --- /dev/null +++ b/hmmer-reader/test/corrupted6.hmm @@ -0,0 +1,32 @@ +HMMER3/f [3.3.1 | Jul 2020] +NAME 1-cysPrx_C +ACC PF10417.10 +DESC C-terminal domain of 1-Cys peroxiredoxin +LENG 40 +ALPH amino +RF no +MM no +CONS yes +CS yes +MAP yes +DATE Sat Apr 18 11:53:25 2020 +NSEQ 43 +EFFN 18.158997 +CKSUM 3953450312 +GA 21.10 21.10 +TC 21.10 21.10 +NC 21.00 21.00 +STATS LOCAL MSV -7.4634 0.71948 +STATS LOCAL VITERBI -7.8384 0.71948 +STATS LOCAL FORWARD -4.3248 0.71948 +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 + COMPO 2.27455 4.34880 2.81236 2.64173 3.87711 2.69981 3.89971 3.31427 2.55515 2.85878 4.03181 3.23004 2.53005 2.90544 3.31837 2.93059 2.71936 2.60036 3.49775 3.83086 + 2.68618 4.42x25 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.00000 * + 1 0.31587 6.18340 6.83374 6.85078 7.11180 2.59795 7.26634 6.62914 6.71625 6.32654 3.30432 5.95368 5.87892 6.73911 6.62719 2.04184 4.87271 5.64306 8.45807 7.48123 1 A - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 2 4.66503 5.98593 6.64131 6.03091 1.97550 5.88281 6.17189 2.24753 5.82991 0.67731 2.90319 6.05093 6.14278 5.85183 5.79751 5.21295 4.88544 2.64552 3.19951 3.37566 2 L - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 diff --git a/hmmer-reader/test/corrupted7.hmm b/hmmer-reader/test/corrupted7.hmm new file mode 100644 index 0000000..908cd2d --- /dev/null +++ b/hmmer-reader/test/corrupted7.hmm @@ -0,0 +1,29 @@ +NAME 1-cysPrx_C +ACC PF10417.10 +DESC C-terminal domain of 1-Cys peroxiredoxin +LENG 40 +ALPH amino +RF no +MM no +CONS yes +CS yes +MAP yes +DATE Sat Apr 18 11:53:25 2020 +NSEQ 43 +EFFN 18.158997 +CKSUM 3953450312 +STATS LOCAL MSV -7.4634 0.71948 +STATS LOCAL VITERBI -7.8384 0.71948 +STATS LOCAL FORWARD -4.3248 0.71948 +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 + COMPO 2.27455 4.34880 2.81236 2.64173 3.87711 2.69981 3.89971 3.31427 2.55515 2.85878 4.03181 3.23004 2.53005 2.90544 3.31837 2.93059 2.71936 2.60036 3.49775 3.83086 + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.00000 * + 1 0.31587 6.b8340 6.83374 6.85078 7.11180 2.59795 7.26634 6.62914 6.71625 6.32654 3.30432 5.95368 5.87892 6.73911 6.62719 2.04184 4.87271 5.64306 8.45807 7.48123 1 A - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 + 2 4.66503 5.98593 6.64131 6.03091 1.97550 5.88281 6.17189 2.24753 5.82991 0.67731 2.90319 6.05093 6.14278 5.85183 5.79751 5.21295 4.88544 2.64552 3.19951 3.37566 2 L - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.48576 0.95510 +// diff --git a/hmmer-reader/test/corrupted8.hmm b/hmmer-reader/test/corrupted8.hmm new file mode 100644 index 0000000..5b26eb2 --- /dev/null +++ b/hmmer-reader/test/corrupted8.hmm @@ -0,0 +1,13 @@ +HMMER3/f [3.3.1 | Jul 2020] +NAME 1-cysPrx_C +ACC PF10417.10 +DESC C-terminal domain of 1-Cys peroxiredoxin +LENG 40 +ALPH amino +DATE Sat Apr 18 11:53:25 2020 +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 d->m d->d + COMPO 2.27455 4.34880 2.81236 2.64173 3.87711 2.69981 3.89971 3.31427 2.55515 2.85878 4.03181 3.23004 2.53005 2.90544 3.31837 2.93059 2.71936 2.60036 3.49775 3.83086 + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00218 6.52685 7.24920 0.61958 0.77255 0.00000 * +// diff --git a/hmmer-reader/test/empty.hmm b/hmmer-reader/test/empty.hmm new file mode 100644 index 0000000..e69de29 diff --git a/hmmer-reader/test/three-profs.hmm b/hmmer-reader/test/three-profs.hmm new file mode 100644 index 0000000..9d7bec7 --- /dev/null +++ b/hmmer-reader/test/three-profs.hmm @@ -0,0 +1,2259 @@ +HMMER3/f [3.1b2 | February 2015] +NAME 1-cysPrx_C +ACC PF10417.9 +DESC C-terminal domain of 1-Cys peroxiredoxin +LENG 40 +ALPH amino +RF no +MM no +CONS yes +CS yes +MAP yes +DATE Thu Aug 2 10:53:47 2018 +NSEQ 46 +EFFN 19.774048 +CKSUM 4280830619 +GA 21.10 21.10; +TC 21.10 21.10; +NC 21.00 21.00; +BM hmmbuild HMM.ann SEED.ann +SM hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq +STATS LOCAL MSV -7.4476 0.71948 +STATS LOCAL VITERBI -7.8642 0.71948 +STATS LOCAL FORWARD -4.3200 0.71948 +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 + COMPO 2.29746 4.28487 2.80871 2.63259 3.88407 2.70553 3.90049 3.29909 2.55675 2.84401 4.05223 3.18565 2.53051 2.95496 3.34479 2.92223 2.70924 2.58911 3.50142 3.82158 + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00201 6.60846 7.33081 0.61958 0.77255 0.00000 * + 1 0.34643 6.26452 6.93341 6.96020 7.21084 2.62977 7.36110 6.73244 6.81955 6.42888 3.33286 6.03968 5.96034 6.83607 6.72157 1.84723 4.95439 5.73250 8.55485 7.58384 1 A - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00201 6.60846 7.33081 0.61958 0.77255 0.48576 0.95510 + 2 4.76564 6.08382 6.74086 6.13136 2.02430 5.98526 6.26781 2.17180 5.93119 0.68037 2.92792 6.15256 6.24010 5.94756 5.89683 5.31642 4.98545 2.72416 3.24423 3.05758 2 L - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00201 6.60846 7.33081 0.61958 0.77255 0.48576 0.95510 + 3 4.11928 6.56003 3.60907 3.81885 5.93418 4.86900 3.83133 3.91951 2.21829 3.63701 5.60597 4.34117 5.25079 0.50584 2.72101 4.08484 3.60796 4.96911 6.94493 5.59487 3 Q - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00201 6.60846 7.33081 0.61958 0.77255 0.48576 0.95510 + 4 2.75821 5.37988 5.94807 3.36995 1.91280 5.16972 2.42086 3.81171 5.12281 1.57880 2.73109 5.32625 5.53357 5.25738 5.13730 4.48024 1.82152 2.36221 6.00120 2.75432 4 l - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00201 6.60846 7.33081 0.61958 0.77255 0.48576 0.95510 + 5 1.46161 5.77180 4.74508 4.18714 4.96279 3.04445 3.20520 4.33300 4.15499 4.03084 4.90960 3.20560 5.29489 4.46900 4.53826 2.15004 1.72818 1.57099 6.38020 3.87770 5 a - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00201 6.60846 7.33081 0.61958 0.77255 0.48576 0.95510 + 6 2.28540 6.36388 0.94350 1.97177 5.70890 4.62689 4.81407 5.19481 3.15080 4.66910 3.74328 4.09437 5.02048 3.10372 2.96915 3.28991 2.71674 4.75450 3.52687 5.38564 6 d - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00201 6.60846 7.33081 0.61958 0.77255 0.48576 0.95510 + 7 2.34626 6.36697 4.10416 1.91432 5.71305 4.62885 4.81506 5.19907 1.23271 4.67228 5.40753 4.09614 5.02221 2.66959 2.15285 2.40505 2.67880 3.90237 6.79869 4.03410 7 k - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00201 6.60846 7.33081 0.61958 0.77255 0.48576 0.95510 + 8 3.00325 6.36517 3.42591 1.89449 3.17188 3.54145 1.74096 5.19796 2.73947 3.48002 5.40556 2.36803 5.01901 3.08407 3.22023 2.65580 2.37126 4.75636 6.79724 2.90503 8 h - - H + 2.68634 4.42241 2.77536 2.73139 3.46370 2.40448 3.72511 3.29370 2.67627 2.69371 4.24706 2.90363 2.73756 3.18162 2.89817 2.37903 2.77536 2.98534 4.58493 3.61519 + 0.08430 2.52331 7.33081 0.07211 2.66539 0.48576 0.95510 + 9 3.99697 6.51575 3.45874 3.63605 5.86358 0.74480 4.93575 5.35106 1.97868 4.81936 5.56181 2.65711 2.97958 3.06890 3.46488 2.86503 4.23048 4.90914 6.94253 5.52860 10 g - - T + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00201 6.60846 7.33081 0.61958 0.77255 0.48576 0.95510 + 10 3.86007 6.29055 3.05255 1.63077 5.60345 3.56272 4.83737 2.54748 2.59360 3.11462 5.33984 3.20397 5.03926 3.94517 3.25579 2.89302 4.09128 1.17491 6.74294 5.35225 11 v - 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- S + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00206 6.58356 7.30590 0.61958 0.77255 0.78321 0.61053 + 29 2.93150 6.49726 2.07178 3.27730 5.84090 4.69591 4.92605 5.33092 3.31855 4.80468 5.54767 4.16241 3.07343 3.38290 4.18807 1.37877 1.09758 4.88908 6.93411 5.51358 42 t - - S + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00206 6.58356 7.30590 0.61958 0.77255 0.78321 0.61053 + 30 3.18813 4.08603 2.52929 2.06383 3.44606 4.61663 4.00929 3.77140 3.54732 3.81979 5.35002 2.97669 2.22127 2.07033 3.18427 2.84132 2.99416 2.83873 6.74797 2.28502 43 e - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00206 6.58356 7.30590 0.61958 0.77255 0.33656 1.25255 + 31 3.90290 6.42159 1.49730 1.12623 5.76652 3.71450 3.35689 5.25508 2.14463 4.72677 5.46347 2.81974 5.06014 2.59053 4.09619 3.86154 3.64817 3.79991 6.85298 5.43767 44 e - 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- H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00206 6.58356 7.30590 0.61958 0.77255 0.33656 1.25255 + 35 2.21160 4.14958 3.04456 2.13603 5.71165 3.16032 4.81240 5.19843 1.10490 3.73886 5.40579 3.27152 5.01896 2.50006 3.56530 3.06867 3.20374 4.75669 3.35591 5.38579 50 k - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00201 6.60846 7.33081 0.61958 0.77255 0.48576 0.95510 + 36 3.29195 4.30629 2.37879 1.70193 5.71218 3.92078 3.28587 5.19907 2.35289 3.84671 4.03940 3.11450 5.01888 3.20079 1.21446 3.34380 3.32353 4.75714 6.79769 5.38595 51 r - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00201 6.60846 7.33081 0.61958 0.77255 0.48576 0.95510 + 37 3.34408 5.37936 5.95125 3.54471 2.17309 5.17003 5.50280 3.36485 5.12502 1.62875 2.82404 5.32763 5.53386 3.66266 4.00159 4.48068 3.38835 2.62225 6.00087 1.09060 52 y - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02608 6.60846 3.71360 0.61958 0.77255 0.48576 0.95510 + 38 3.84745 3.95769 3.54353 2.50475 2.40046 3.34558 4.84525 3.19916 2.22323 1.81552 5.24776 4.14802 2.71798 2.15255 3.55116 2.92879 3.13967 4.54571 2.82980 5.29365 53 l - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00205 6.58444 7.30678 0.61958 0.77255 0.77417 0.61820 + 39 2.91087 6.35819 2.73825 1.37250 5.70436 2.65638 4.80252 5.19164 2.23483 4.66395 5.39880 2.35774 5.00826 2.73738 4.03198 2.04894 2.40406 4.74946 6.78998 5.37749 54 e - - H + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00205 6.58444 7.30678 0.61958 0.77255 0.34020 1.24351 + 40 3.29199 6.36444 3.46625 2.89528 5.71020 1.17635 4.01569 5.19665 1.96763 2.89634 5.40492 2.59522 5.01920 3.04143 3.67726 2.85657 2.47447 3.90905 6.79671 3.78781 55 g - - T + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.00135 6.60780 * 0.61958 0.77255 0.00000 * +// +HMMER3/f [3.1b2 | February 2015] +NAME 120_Rick_ant +ACC PF12574.8 +DESC 120 KDa Rickettsia surface antigen +LENG 235 +ALPH amino +RF no +MM no +CONS yes +CS no +MAP yes +DATE Thu Aug 2 13:19:42 2018 +NSEQ 4 +EFFN 0.753906 +CKSUM 3014919924 +GA 25.00 25.00; +TC 28.40 28.20; +NC 23.50 22.30; +BM hmmbuild HMM.ann SEED.ann +SM hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq +STATS LOCAL MSV -10.6539 0.70354 +STATS LOCAL VITERBI -11.6345 0.70354 +STATS LOCAL FORWARD -5.3865 0.70354 +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 + COMPO 2.47491 4.58645 2.83243 2.53739 3.43810 2.90546 3.72487 2.90137 2.54344 2.57426 3.72691 2.96472 3.44309 2.97553 3.09033 2.62160 2.75444 2.69892 4.81523 3.46896 + 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503 + 0.02633 4.04589 4.76824 0.61958 0.77255 0.00000 * + 1 3.26601 4.58151 4.85941 4.33466 3.23284 4.55382 4.92596 1.38530 4.16872 1.18692 3.05183 4.58243 4.77976 4.36089 4.31534 3.92939 3.50539 1.96630 5.28692 4.14252 1 l - 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