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use local files for testing
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@horta
horta committed Aug 16, 2023
1 parent 3f3540d commit 2e038ab
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Showing 11 changed files with 3,611 additions and 36 deletions.
46 changes: 10 additions & 36 deletions hmmer-reader/test/CMakeLists.txt
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@@ -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})
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563 changes: 563 additions & 0 deletions hmmer-reader/test/corrupted1.hmm
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522 changes: 522 additions & 0 deletions hmmer-reader/test/corrupted2.hmm
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146 changes: 146 additions & 0 deletions hmmer-reader/test/corrupted3.hmm
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33 changes: 33 additions & 0 deletions hmmer-reader/test/corrupted4.hmm
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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
//
4 changes: 4 additions & 0 deletions hmmer-reader/test/corrupted5.hmm
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HMMER3/f [3.3.1 | Jul 2020]
NAME 1-cysPrx_C
ACC PF10417.10
//
32 changes: 32 additions & 0 deletions hmmer-reader/test/corrupted6.hmm
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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
29 changes: 29 additions & 0 deletions hmmer-reader/test/corrupted7.hmm
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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
//
13 changes: 13 additions & 0 deletions hmmer-reader/test/corrupted8.hmm
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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 *
//
Empty file added hmmer-reader/test/empty.hmm
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