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Commit 14cce39a authored by Gustaf Ahdritz's avatar Gustaf Ahdritz
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Add data pipeline test

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tests/test_data/alignment/bfd_uniclust_hits.a3m deleted 100644 → 0
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tests/test_data/alignment/mgnify_hits.sto deleted 100644 → 0
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# STOCKHOLM 1.0
#=GF ID query-i1
#=GF AU jackhmmer (HMMER 3.3.2)
#=GS MGYP000406148242/1-68 DE [subseq from] PL=00 UP=0 BIOMES=0101000000000
#=GS MGYP000119383271/47-117 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000430010134/3-69 DE [subseq from] PL=00 UP=0 BIOMES=0000110000000
#=GS MGYP000184282189/1-71 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000372988949/3-70 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000222615028/3-68 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000384795733/25-88 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000680660046/4-73 DE [subseq from] PL=00 UP=0 BIOMES=0000110000000
#=GS MGYP000586297297/4-70 DE [subseq from] PL=00 UP=0 BIOMES=0000110000000
#=GS MGYP000526302968/5-69 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000081082088/4-68 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000172493671/1-71 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000694390052/2-70 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000246175980/4-68 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000358235060/4-70 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000635416234/5-68 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000656061151/3-65 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000718018739/4-64 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000234420019/4-70 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000689530757/1-71 DE [subseq from] PL=00 UP=0 BIOMES=0000100000000
#=GS MGYP000266820214/24-89 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000190165740/1-71 DE [subseq from] PL=00 UP=0 BIOMES=0000000000001
#=GS MGYP000589249599/4-69 DE [subseq from] PL=00 UP=0 BIOMES=0000110000000
#=GS MGYP000048618675/3-70 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000377290797/1-69 DE [subseq from] PL=00 UP=1 BIOMES=0110000000000
#=GS MGYP000697367932/3-70 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000747506700/4-68 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000255037255/6-64 DE [subseq from] PL=10 UP=0 BIOMES=0000101000000
#=GS MGYP000602985373/3-68 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000420186793/4-69 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000452617499/5-64 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000119404247/1-68 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000134149386/3-60 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000461455637/26-91 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000119389418/96-161 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000546988737/26-93 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000624371167/1-68 DE [subseq from] PL=00 UP=0 BIOMES=0101000000000
#=GS MGYP000650157322/5-70 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000246214200/7-73 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000113479303/34-96 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000187226991/3-69 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000381848663/3-69 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000066325489/28-89 DE [subseq from] PL=00 UP=0 BIOMES=0000000000001
#=GS MGYP000013251582/4-69 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000499794189/19-84 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000555816272/4-69 DE [subseq from] PL=00 UP=0 BIOMES=0000000000001
#=GS MGYP000653248377/3-70 DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
#=GS MGYP000113511630/3-70 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP001057101778/4-69 DE [subseq from] PL=00 UP=0 BIOMES=1000000000000
#=GS MGYP000210824545/3-69 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000676742083/9-64 DE [subseq from] PL=10 UP=0 BIOMES=0000101000000
#=GS MGYP000545010933/4-70 DE [subseq from] PL=00 UP=0 BIOMES=0000110000000
#=GS MGYP000541064880/3-68 DE [subseq from] PL=00 UP=0 BIOMES=0000000000001
#=GS MGYP000541064880/99-161 DE [subseq from] PL=00 UP=0 BIOMES=0000000000001
#=GS MGYP000729801087/3-52 DE [subseq from] PL=10 UP=0 BIOMES=0000101000000
#=GS MGYP000715079888/40-96 DE [subseq from] PL=10 UP=0 BIOMES=0000101000000
#=GS MGYP000033872322/3-43 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
#=GS MGYP000464421157/4-69 DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
query MAAHKGAEHHHK-AAEHHEQAAKHHHAAAEHHEKGE-HEQAAHHADTAYAHHKHAEEHAAQAAKHD-AEHHAPKPH
MGYP000406148242/1-68 MATHKGAESHKK-AAEHHTTAAKHHTEAAKSHESGN-HEKAAHHAHTATAHGKHASDHSDDAAKTY-ASEH-----
#=GR MGYP000406148242/1-68 PP 899*********.***********************.***************************98.8877.....
MGYP000119383271/47-117 MATHKGTEHHKK-AAEHHELAAKHHREAAKLHEAGS-HEKAAHHAQIAAGHGLHAVYHTEEATKHH-ADEHTGK--
#=GR MGYP000119383271/47-117 PP 899*********.***********************.*****************************.**99866..
MGYP000430010134/3-69 ---KKAAEHHRK-AAEHHQNAAKHHNAAAESHEAGN-HEKAAHHAHTAHGHHTQAGEHGGEAAKAH-RDEHGQ---
#=GR MGYP000430010134/3-69 PP ...699******.***********************.***************************88.877765...
MGYP000184282189/1-71 MPKHEGAEHHKK-AAEHHEKAAQHHKEAAKHHEEGR-HETAGHHAYVAHGHHLTAIQHSEEAAKYH-SQQHGEK--
#=GR MGYP000184282189/1-71 PP 568*********.***********************.****************************9.9999876..
MGYP000372988949/3-70 ---KKAAEHHLK-AAEHHEHAARHHKEAAKHHQAGS-YEKAAHHAHTARAHAEHADEHAVEAAKAH-AEEHGSK--
#=GR MGYP000372988949/3-70 PP ...699******.***********************.*****************************.**99865..
MGYP000222615028/3-68 ---KKAVEHHHK-AAEHHEHAARHHKEAAKHHEAGK-HETAAHHAHLARGHHEHAMHHAAEAAKAH-VEDHG----
#=GR MGYP000222615028/3-68 PP ...6899*****.***********************.***************************99.99986....
MGYP000384795733/25-88 ----SGSQQHDA-AAQHYEEAARHHRQAAKHYQASR-HEKAAHHAQLGYAHHLYAEQHAAEAAKAH-AKNH-----
#=GR MGYP000384795733/25-88 PP ....6999****.***********************.***************************99.9998.....
MGYP000680660046/4-73 -STHKGAEHHKE-AAAHHKKAAEHHLAAAEHHEAGD-HEKAGHHAHVAHGHHLNAVHHAEEAGKHHGAEHSGP---
#=GR MGYP000680660046/4-73 PP .57*********.***********************.**************************9752788777...
MGYP000586297297/4-70 ----QAAEHHQK-AAEHHEHAARHHREAAAHHEEGN-HETAAHHAHTAQGHLHHATHHASEAAKHH-VEHHGNK--
#=GR MGYP000586297297/4-70 PP ....689*****.***********************.*****************************.****977..
MGYP000526302968/5-69 -----REEHHLK-AAEHHEHAAKHHLAAAEHHAGGD-HEKAGHHAHVAHGHSTHAEHHAEEASKHT-ANHDAA---
#=GR MGYP000526302968/5-69 PP .....469999*.***********************.*****************************.***985...
MGYP000081082088/4-68 ----QAAEHHHK-AAEHHEHAARHHKEAAKHHEAGK-HETAAHHAHLARGHHEHAMHHAAEAAKAH-IQDHG----
#=GR MGYP000081082088/4-68 PP ....689*****.***********************.**************************977.66664....
MGYP000172493671/1-71 MTKHEGAEHHKQ-AAQQHQDAARHHLEAAKHHEAGA-HEKAGHHAHIAYGHHLQATHHAEEAAKHH-AMQHGDK--
#=GR MGYP000172493671/1-71 PP 678*********.***********************.*****************************.*999876..
MGYP000694390052/2-70 --SHAAAEHHKK-AAEHHEHAARHHQEAAKHHEAGN-HEKAAHHAHVAHGHHVHAVEHAEHAAKHH-AETHGAK--
#=GR MGYP000694390052/2-70 PP ..699*******.***********************.*****************************.**99865..
MGYP000246175980/4-68 ----QAAEHHHK-AAEHHEHAARHHKEAAKHHEAGK-HETAAHHAHLARGHHVHAMHHAGEAAKAH-IEDHG----
#=GR MGYP000246175980/4-68 PP ....689*****.***********************.***************************88.88885....
MGYP000358235060/4-70 ----QAAEHHGK-AAEHHEHAARHHREAANHHEAGD-HQQAAHHAHTAQGHLHHATHHSAEAAKLH-VEHHGHK--
#=GR MGYP000358235060/4-70 PP ....689*****.***********************.*****************************.****877..
MGYP000635416234/5-68 -----VADHHHK-AAEHHERAAKHHREAATHYESDR-HETAAHHAHMAHGHHQHAVHHASEAAKAH-IEHHD----
#=GR MGYP000635416234/5-68 PP .....489****.***********************.*****************************.****6....
MGYP000656061151/3-65 ---KKAAEHHRK-AAEHHEHAARHHKEAAKHHDAGA-HEKAAHHAHTAHAHHLHATHFADEAAKAH-AD-------
#=GR MGYP000656061151/3-65 PP ...699******.***********************.**************************977.75.......
MGYP000718018739/4-64 -----GAKHHNA-AAQHYEEAARHHRKAAELYQCGH-HEKVSHHANLASGHPLHAKQHAEEAAKAL-IE-------
#=GR MGYP000718018739/4-64 PP .....99*****.***********************.**************************976.55.......
MGYP000234420019/4-70 ----AAAEHHRK-AAEHHEHAARHHEEAAEHHESGA-HETAAHHAHSAQGHTHHALYHASEAAKEH-AEHHGDK--
#=GR MGYP000234420019/4-70 PP ....479*****.***********************.*****************************.****875..
MGYP000689530757/1-71 MPTHTGAEHHRK-AAEHHQLAAKHHLEAAKLHDAGS-HEKAAHHSEIAAGHGHHAVYHTEEATKQH-ADMNAEK--
#=GR MGYP000689530757/1-71 PP 578*********.***********************.****************************9.9999877..
MGYP000266820214/24-89 ---KKAAEHHLK-AAEHHEHAARHHKEAAKHHQAGS-HEKAAHHAHTARAHEEHAEFHSAEAAKAH-GQEHG----
#=GR MGYP000266820214/24-89 PP ...699******.***********************.**************************977.77775....
MGYP000190165740/1-71 MARHEGAEHHKQ-AAEHHQHAARHHLEAAKHHEAGA-HEKAGHHAHIAQGHHLHAIHHAEEAAKHH-AAQHGDK--
#=GR MGYP000190165740/1-71 PP 799*********.***********************.*****************************.*999876..
MGYP000589249599/4-69 ----QAAEHHTK-AAEHHQHAARHHLEAAKHHEAGR-HEAAGHHAHLAHGHHQHATHHASEAAKSH-IEHHGK---
#=GR MGYP000589249599/4-69 PP ....689*****.***********************.*****************************.****75...
MGYP000048618675/3-70 ---KKASEHHRK-AAEHHKLAATHHEEAAAHYDKGN-HEKAAHHAHVAHGHTLHATHYAAEAAKMH-VEEHGSK--
#=GR MGYP000048618675/3-70 PP ...6899*****.***********************.***************************99.9999866..
MGYP000377290797/1-69 MSDHAGVEHYHK-AAEHHEHAARHHREAAKHHEEGN-HEKAAHHAHSAHGHASHAQHHHTEASRHH-AEHHG----
#=GR MGYP000377290797/1-69 PP 678*********.***********************.*****************************.****7....
MGYP000697367932/3-70 ---KKASEHHRK-AAEHHKLAATHHEEAAAHHDKGN-YEKAAHHAHVAHGHTHHATYHAAEAAKIH-AEDYGSK--
#=GR MGYP000697367932/3-70 PP ...6899*****.***********************.***************************99.9988765..
MGYP000747506700/4-68 ----QAAEHHHK-AAEHHEHAALHHKEAAKHHEAGK-HEMAAHHAHLARAHHEHAMHHAVEAVKAH-LQDHG----
#=GR MGYP000747506700/4-68 PP ....689*****.***********************.**************************977.76664....
MGYP000255037255/6-64 ---SKIAEHHTK-AAEHHETAAQHHREAAKHHEAGS-IEKAAHHAQVAYGHGAHAWNYQEEAAK------------
#=GR MGYP000255037255/6-64 PP ...5789*****.***********************.******************999999998............
MGYP000602985373/3-68 ---KKAVEHHNK-AAEHHEHAARHHKEAAKHHEAGK-HETAGHHAHLARGHQEHAMHHSAEAAKAH-IEDHS----
#=GR MGYP000602985373/3-68 PP ...6899*****.***********************.***************************99.98886....
MGYP000420186793/4-69 ----QAAEHHLK-AAEHHEHAAHHHKEAAKHHQGGS-HEKAAHHAHTARGHHEHAQHHAAEAAKAH-AQEHGN---
#=GR MGYP000420186793/4-69 PP ....689*****.***********************.***************************99.999975...
MGYP000452617499/5-64 -----AAAHHLK-AVEHHEHAARHHREAAKHHEAGN-HEKAAHHAHLAHGHHLHATEYAGEAAKAH-I--------
#=GR MGYP000452617499/5-64 PP .....678999*.***********************.**************************965.5........
MGYP000119404247/1-68 MAGHKIHEHHEK-AADHHEHAAKHHREAAKHHKAGD-HEKAAHHSKVAHGHHLHATEHHDEASKKH-AEDH-----
#=GR MGYP000119404247/1-68 PP 799*********.***********************.***************************99.9998.....
MGYP000134149386/3-60 ---KKATEHHRK-AAEHHEHAARHHKEAAKHHEAGK-HETAAHHAHLARGHQERAAQQAAEAA-------------
#=GR MGYP000134149386/3-60 PP ...6899*****.***********************.***********************998.............
MGYP000461455637/26-91 -----AAKHHDL-AAQHYEEAARHHREAAQDYQSGR-HEKASHHAHLAYAHHLHAEQHAEEAAKAH-IKNHLDD--
#=GR MGYP000461455637/26-91 PP .....589****.***********************.***************************99.9999765..
MGYP000119389418/96-161 ---KQAAEHHRK-AAEHHEHAARHHKEAAKHHEAGK-HETAAHHAHLARAHHEVATHHAVEAAKAH-LEEHG----
#=GR MGYP000119389418/96-161 PP ...5689*****.***********************.***************************88.88775....
MGYP000546988737/26-93 ---EKAAEHHEK-AAEHNERAAQHHREAAKHHEEGH-HETAGHHAQIAHGHHLNATHHSEEAAKHH-AQQHGEK--
#=GR MGYP000546988737/26-93 PP ...589******.***********************.*****************************.****876..
MGYP000624371167/1-68 MAKHPGADYHRM-AAEHHEKAALHHKKAAEYYEAGN-LKKAAIHAELAAVFHKQADEHVYNKQEEI-DVHH-----
#=GR MGYP000624371167/1-68 PP 799*********.***********************.*********************98877665.5566.....
MGYP000650157322/5-70 -----ATEHHRR-AAEHHEHSAKHHKAVADHHEAGN-HEKAGHHASVAEGHLNHASHHAEEASKHH-AADHGHK--
#=GR MGYP000650157322/5-70 PP .....579****.***********************.*****************************.9999765..
MGYP000246214200/7-73 ----KIAEHHAQ-AAQHHEKAAEHHKEAAKHYGTGA-VEKGAHHAQVAQGHAVHAEYHADEAAKAH-AEHHAGK--
#=GR MGYP000246214200/7-73 PP ....779*****.***********************.*****************************.****976..
MGYP000113479303/34-96 --NHKGIENHRK-AAKHHEEAAKHHHDAAKHHEAGN-HDKACESTVKAHGHHCLASDHMREVSKQH-A--------
#=GR MGYP000113479303/34-96 PP ..5*********.***********************.**********************9999875.5........
MGYP000187226991/3-69 ---KKAADHHKQ-AAEHHTHAAKHHTEAARHHESGN-HEKAAHHAHSSRAHASQADDHAEQAAKAH-MDEHGK---
#=GR MGYP000187226991/3-69 PP ...689******.***********************.***************************88.888865...
MGYP000381848663/3-69 ---KKAAEHHHK-ASEHHTHAARHHSEAAKHHEGGH-HEKAAHHAHTARAHALHSRHHSDEAAKMH-GEEHGK---
#=GR MGYP000381848663/3-69 PP ...699******.***********************.***************************99.999876...
MGYP000066325489/28-89 ----KTIANHKQ-AARHHMEAAKHHMEAARHHEEGN-HEKAAHSTLLAYGHHTIAGEFVSDDAKHH-AQ-------
#=GR MGYP000066325489/28-89 PP ....56678999.***********************.********************999999988.75.......
MGYP000013251582/4-69 ----EAANHHKQ-AAEHHEHAARHHHEAAKHHLAGN-HEKAAHHAHLAHGHHVHATEHAENAAKEH-VKAHGA---
#=GR MGYP000013251582/4-69 PP ....57889999.***********************.***************************99.888865...
MGYP000499794189/19-84 ---NDAAEHHRK-AAEHHEHAAAHHREAAEHHANGN-HEKAAHHAHIAHGHGLHAAHHAGEATKHH-ANTHG----
#=GR MGYP000499794189/19-84 PP ...5689*****.***********************.*****************************.*9986....
MGYP000555816272/4-69 -----EAAHHHKQAAEHHEHAARHHHEAAKHHEAGN-HEKAAHHAHLAHAHHVLAAEHAENAAKEH-LKAHGT---
#=GR MGYP000555816272/4-69 PP .....4555554399*********************.***************************99.888865...
MGYP000653248377/3-70 ---KKAAEHHKK-ASEHLTHAARHHGEAAKHHEAGS-HEKAAHHAHTARAHIIHGRGHAEEAVKAH-AEEHGKK--
#=GR MGYP000653248377/3-70 PP ...699******.***********************.*****************************.**99865..
MGYP000113511630/3-70 ---KKAAEHHRK-AAEHHKHAAGHHEEAAAHHDKGN-HEKAAHHAHVAHGHTLHAAHHAEEAAKAH-VEEHGSK--
#=GR MGYP000113511630/3-70 PP ...699******.***********************.***************************99.9999866..
MGYP001057101778/4-69 ---DKIIEHHRS-AADHHEKAAQHHREAAKHHASDS-HEKAAHHAHSAHGHSAHATHHAGEASKHH-AEHHG----
#=GR MGYP001057101778/4-69 PP ...5678*****.***********************.*****************************.****6....
MGYP000210824545/3-69 ---KKAAESHKK-ASEHLTHAARHHTEAAKHHETGQ-HEKAAHHAHIARAHATHAREHSENAAKAH-LEEHGK---
#=GR MGYP000210824545/3-69 PP ...689******.***********************.***************************99.999976...
MGYP000676742083/9-64 ------RDEHNK-AAEHHENAAKAHRSAAEHHGKGD-HAKGKQHADTAKQHSQTAHQHTDQAHS------------
#=GR MGYP000676742083/9-64 PP ......5789**.***********************.**********************99854............
MGYP000545010933/4-70 --KHPSTEHHTS-AAEEHDNASRHHRAAAKNYEEGK-HETAAHHAHSASGHSSNARDQAEEASRKH-AKQHG----
#=GR MGYP000545010933/4-70 PP ..58999*****.***********************.*************************9888.88775....
MGYP000541064880/3-68 -AEHNAAEHHGF-AAHHHQRAAQFHREASRHYEAGKDYAHAAHQALVAHGHALLAIDHGNEAGKYY-AG-------
#=GR MGYP000541064880/3-68 PP .789********.*********************963789***********************997.64.......
MGYP000541064880/99-161 ------SEHHAA-AADDHEQAAQHHAQAAKHLNEKD-YELAAHEAQLAHRHAHYSIFHDDEAAKHH-VEHYG----
#=GR MGYP000541064880/99-161 PP ......69****.***********************.**************999************.***86....
MGYP000729801087/3-52 ---KKVAEHHLK-AAEHLEHAARHHKEAAKHHEAGN-HEKAAHHAHIARAHHEHA---------------------
#=GR MGYP000729801087/3-52 PP ...5889*****.***********************.*****************7.....................
MGYP000715079888/40-96 -----SAEYHKK-AANCHYEAAKHHNIAAKHHEAGN-HKKASEYALKAYWYHCLASEAEKEDVK------------
#=GR MGYP000715079888/40-96 PP .....69*****.***********************.***************998876655555............
MGYP000033872322/3-43 ---KKAAEHHRK-AAEHHEHAARHHKEAAKHHDAGA-HEKAAHHAH------------------------------
#=GR MGYP000033872322/3-43 PP ...699******.***********************.*******96..............................
MGYP000464421157/4-69 ----EAAEHHKH-AAEHLTHAARHHSEAAKHHEAGQ-HEKAAHHAHLAHGHQEHASEHAVEAAKKH-IEAHGN---
#=GR MGYP000464421157/4-69 PP ....689*****.***********************.***************************99.999875...
#=GC PP_cons 7887889*****.***********************.**************************999.9998766..
#=GC RF xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx
//
tests/test_data/alignment/pdb70_hits.hhr deleted 100644 → 0
View file @ f9dc8b15
Query query
Match_columns 73
No_of_seqs 55 out of 57
Neff 2.88591
Searched_HMMs 80799
Date Thu Dec 30 19:40:02 2021
Command /home/ga122/openfold/lib/conda/envs/openfold_venv/bin/hhsearch -i /tmp/tmpedq9nsbw/query.a3m -o /tmp/tmpedq9nsbw/output.hhr -maxseq 1000000 -d /data/ga122/alphafold/pdb70/pdb70
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1HF9_B ATPASE INHIBITOR (MITOC 7.5 3.8E+02 0.0047 16.2 0.0 22 7-28 10-31 (41)
2 2CRB_A nuclear receptor bindin 6.4 4.7E+02 0.0058 18.0 0.0 20 11-30 32-51 (97)
3 4ZEY_A nuclear receptor bindin 6.3 4.7E+02 0.0059 17.3 0.0 20 11-30 26-45 (84)
4 3U8V_A Metal-binding protein s 4.1 8.1E+02 0.01 17.3 0.0 32 15-46 50-81 (93)
5 1PSM_A SPAM-H1 (RESIDUES 90 - 1.9 2.1E+03 0.026 13.4 0.0 18 11-28 14-31 (38)
6 5KC1_F Autophagy-related prote 1.5 2.7E+03 0.033 16.9 0.0 17 12-28 25-41 (226)
7 5KC1_J Autophagy-related prote 1.5 2.7E+03 0.033 16.9 0.0 17 12-28 25-41 (226)
8 3ZEE_A PARTITIONING DEFECTIVE 1.1 3.8E+03 0.046 12.5 0.0 15 58-72 30-44 (84)
9 4I6P_A Partitioning defective 1.0 4.3E+03 0.054 12.4 0.0 16 57-72 32-47 (88)
10 2Q2K_A Hypothetical protein/DN 1.0 4.3E+03 0.054 13.4 0.0 17 56-72 54-70 (70)
No 1
>1HF9_B ATPASE INHIBITOR (MITOCHONDRIAL); ATPASE INHIBITOR, F1 ATPASE INHIBITOR; NMR {BOS TAURUS} SCOP: h.4.8.1
Probab=7.51 E-value=3.8e+02 Score=16.19 Aligned_cols=22 Identities=23% Similarity=0.398 Sum_probs=13.1 Template_Neff=4.500
Q query 7 AEHHHKAAEHHEQAAKHHHAAA 28 (73)
Q Consensus 7 aEhH~kAAeHHe~AA~HH~eAA 28 (73)
.++|++-++.|+.|.+-|++-.
T Consensus 10 I~~He~qIk~heeaI~RHk~~i 31 (41)
T 1HF9_B 10 ISHHAKEIERLQKEIERHKQSI 31 (41)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666666666666665543
No 2
>2CRB_A nuclear receptor binding factor 2; NRBF-2, MIT domain, helix bundle; NMR {Mus musculus} SCOP: a.7.16.1
Probab=6.35 E-value=4.7e+02 Score=18.01 Aligned_cols=20 Identities=20% Similarity=0.165 Sum_probs=11.0 Template_Neff=5.700
Q query 11 HKAAEHHEQAAKHHHAAAEH 30 (73)
Q Consensus 11 ~kAAeHHe~AA~HH~eAAkH 30 (73)
..|++-|.+|++...+|.+-
T Consensus 32 ~~Aie~H~kAA~~f~~A~~~ 51 (97)
T 2CRB_A 32 EEAISCHRKATTYLSEAMKL 51 (97)
T ss_dssp HHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHc
Confidence 34555556666555555543
No 3
>4ZEY_A nuclear receptor binding factor 2; Structural Genomics, Joint Center for; HET: SO4, MSE; 1.5A {Homo sapiens}
Probab=6.31 E-value=4.7e+02 Score=17.29 Aligned_cols=20 Identities=25% Similarity=0.200 Sum_probs=10.8 Template_Neff=6.200
Q query 11 HKAAEHHEQAAKHHHAAAEH 30 (73)
Q Consensus 11 ~kAAeHHe~AA~HH~eAAkH 30 (73)
..|++-|.+|+....+|.+-
T Consensus 26 ~~A~e~H~~AA~~f~~A~~~ 45 (84)
T 4ZEY_A 26 EEAISCHKKAAAYLSEAMKL 45 (84)
T ss_dssp HHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 44555555555555555543
No 4
>3U8V_A Metal-binding protein smbP; four helical bundle, metal chaperone; 1.9A {Nitrosomonas europaea}
Probab=4.11 E-value=8.1e+02 Score=17.29 Aligned_cols=32 Identities=34% Similarity=0.433 Sum_probs=15.8 Template_Neff=4.400
Q query 15 EHHEQAAKHHHAAAEHHEKGEHEQAAHHADTA 46 (73)
Q Consensus 15 eHHe~AA~HH~eAAkHheaG~HekAahhAh~A 46 (73)
+|-..+.++-.+|.++-..|+-+.|..++-.|
T Consensus 50 ~H~~~aik~LeeAI~hgk~ghad~A~kha~~A 81 (93)
T 3U8V_A 50 THVGHGIKHLEDAIKHGEEGHVGVATKHAQEA 81 (93)
T ss_dssp CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHH
Confidence 34444455555555555555555544444433
No 5
>1PSM_A SPAM-H1 (RESIDUES 90 - 127; POLYMORPHIC ANTIGEN; NMR {Plasmodium falciparum} SCOP: j.18.1.1
Probab=1.89 E-value=2.1e+03 Score=13.41 Aligned_cols=18 Identities=39% Similarity=0.433 Sum_probs=8.0 Template_Neff=1.300
Q query 11 HKAAEHHEQAAKHHHAAA 28 (73)
Q Consensus 11 ~kAAeHHe~AA~HH~eAA 28 (73)
.+|++--|+|++.=.+|+
T Consensus 14 e~aa~dae~a~k~ae~a~ 31 (38)
T 1PSM_A 14 EQAAKDAENASKEAEEAA 31 (38)
T ss_dssp HSTTTTTTHHHHHTTTTT
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 444444444444444443
No 6
>5KC1_F Autophagy-related protein 38; Atg38, coiled-coil, dimerization, NRBF2, autophagy; HET: NO3, NH4, EDO, NA; 2.2A {Saccharomyces cerevisiae}
Probab=1.52 E-value=2.7e+03 Score=16.87 Aligned_cols=17 Identities=12% Similarity=0.040 Sum_probs=0.0 Template_Neff=5.100
Q query 12 KAAEHHEQAAKHHHAAA 28 (73)
Q Consensus 12 kAAeHHe~AA~HH~eAA 28 (73)
.|++-|.+|++.-.+|.
T Consensus 25 eAie~h~kAAe~l~~a~ 41 (226)
T 5KC1_F 25 NAKAKYQEAIEVLGPQN 41 (226)
T ss_dssp -----------------
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34444444444444443
No 7
>5KC1_J Autophagy-related protein 38; Atg38, coiled-coil, dimerization, NRBF2, autophagy; HET: NA, NO3, EDO, NH4; 2.2A {Saccharomyces cerevisiae}
Probab=1.52 E-value=2.7e+03 Score=16.87 Aligned_cols=17 Identities=12% Similarity=0.040 Sum_probs=0.0 Template_Neff=5.100
Q query 12 KAAEHHEQAAKHHHAAA 28 (73)
Q Consensus 12 kAAeHHe~AA~HH~eAA 28 (73)
.|++-|.+|++.-.+|.
T Consensus 25 eAie~h~kAAe~l~~a~ 41 (226)
T 5KC1_J 25 NAKAKYQEAIEVLGPQN 41 (226)
T ss_dssp -----------------
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34444444444444443
No 8
>3ZEE_A PARTITIONING DEFECTIVE 3 HOMOLOG; CELL CYCLE; 6.1A {RATTUS NORVEGICUS}
Probab=1.14 E-value=3.8e+03 Score=12.49 Aligned_cols=15 Identities=27% Similarity=0.237 Sum_probs=7.4 Template_Neff=7.600
Q query 58 AQAAKHDAEHHAPKP 72 (73)
Q Consensus 58 ~eAak~ha~~H~~kp 72 (73)
.+|.+.|....+.+|
T Consensus 30 ~~a~~Ry~~~~~~~~ 44 (84)
T 3ZEE_A 30 QQAVTRYRKAVAKDP 44 (84)
T ss_dssp HHHHHHHHHHHCSSS
T ss_pred HHHHHHHHHHcCCCc
Confidence 455555555544433
No 9
>4I6P_A Partitioning defective 3 homolog; PB1 like motif, DUF3534, Cell; 2.9A {Rattus norvegicus}
Probab=1.01 E-value=4.3e+03 Score=12.37 Aligned_cols=16 Identities=25% Similarity=0.206 Sum_probs=0.0 Template_Neff=7.500
Q query 57 AAQAAKHDAEHHAPKP 72 (73)
Q Consensus 57 a~eAak~ha~~H~~kp 72 (73)
+.+|.+.|....+.+|
T Consensus 32 ~~~a~~Ry~~~~~~~~ 47 (88)
T 4I6P_A 32 IQQAVTRYRKAVAKDP 47 (88)
T ss_dssp HHHHHHHHHHHHCCCT
T ss_pred HHHHHHHHHHHcCCCc
No 10
>2Q2K_A Hypothetical protein/DNA Complex; protein-DNA, partition, segregation, parB, DNA; HET: EPE; 3.0A {Staphylococcus aureus}
Probab=1.01 E-value=4.3e+03 Score=13.41 Aligned_cols=17 Identities=24% Similarity=0.343 Sum_probs=0.0 Template_Neff=1.100
Q query 56 HAAQAAKHDAEHHAPKP 72 (73)
Q Consensus 56 Ha~eAak~ha~~H~~kp 72 (73)
|-.||-+.|.++-|..|
T Consensus 54 hireal~ryiee~g~~p 70 (70)
T 2Q2K_A 54 HIREALRRYIEEIGENP 70 (70)
T ss_dssp HHHHHHHHHHHHCCHHC
T ss_pred HHHHHHHHHHHHHCCCC
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# Copyright 2021 AlQuraishi Laboratory
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import pickle
import shutil
import torch
import numpy as np
import unittest
from openfold.data.data_pipeline import DataPipeline
from openfold.data.templates import TemplateHitFeaturizer
from openfold.model.embedders import (
InputEmbedder,
RecyclingEmbedder,
TemplateAngleEmbedder,
TemplatePairEmbedder,
)
import tests.compare_utils as compare_utils
if compare_utils.alphafold_is_installed():
alphafold = compare_utils.import_alphafold()
import jax
import haiku as hk
class TestDataPipeline(unittest.TestCase):
@compare_utils.skip_unless_alphafold_installed()
def test_fasta_compare(self):
# AlphaFold runs the alignments and feature processing at the same
# time, taking forever. As such, we precompute AlphaFold's features
# using scripts/generate_alphafold_feature_dict.py and the default
# databases.
with open("tests/test_data/alphafold_feature_dict.pickle", "rb") as fp:
alphafold_feature_dict = pickle.load(fp)
template_featurizer = TemplateHitFeaturizer(
mmcif_dir="tests/test_data/mmcifs",
max_template_date="2021-12-20",
max_hits=20,
kalign_binary_path=shutil.which("kalign"),
_zero_center_positions=False,
)
data_pipeline = DataPipeline(
template_featurizer=template_featurizer,
)
openfold_feature_dict = data_pipeline.process_fasta(
"tests/test_data/short.fasta",
"tests/test_data/alignments"
)
openfold_feature_dict["template_all_atom_masks"] = openfold_feature_dict["template_all_atom_mask"]
checked = []
# AlphaFold and OpenFold process their MSAs in slightly different
# orders, which we compensate for below.
m_a = alphafold_feature_dict["msa"]
m_o = openfold_feature_dict["msa"]
# The first row of both MSAs should be the same, no matter what
self.assertTrue(np.all(m_a[0, :] == m_o[0, :]))
# Each row of each MSA should appear exactly once somewhere in its
# counterpart
matching_rows = np.all((m_a[:, None, ...] == m_o[None, :, ...]), axis=-1)
self.assertTrue(
np.all(
np.sum(matching_rows, axis=-1) == 1
)
)
checked.append("msa")
# The corresponding rows of the deletion matrix should also be equal
matching_idx = np.argmax(matching_rows, axis=-1)
rearranged_o_dmi = openfold_feature_dict["deletion_matrix_int"]
rearranged_o_dmi = rearranged_o_dmi[matching_idx, :]
self.assertTrue(
np.all(
alphafold_feature_dict["deletion_matrix_int"] ==
rearranged_o_dmi
)
)
checked.append("deletion_matrix_int")
# Remaining features have to be precisely equal
for k, v in alphafold_feature_dict.items():
self.assertTrue(
k in checked or np.all(v == openfold_feature_dict[k])
)
if __name__ == "__main__":
unittest.main()
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