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metaclade2
Commit 3ae3b87d by Riccardo Vicedomini
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added test dataset and a small model subset

parent 115fea16
Showing with 57 additions and 0 deletions
test/pippo/jobs/1_search/pippo_1.sh 0 → 100644
python3 /home/vicedomini/projects/metaclade2/scripts/search_hmm.py PF03441 hmmsearch /home/vicedomini/projects/metaclade2/data/models/HMMs/PF03441.hmm.gz /home/vicedomini/projects/metaclade2/test/test.fa /home/vicedomini/projects/metaclade2/test/pippo/temp /home/vicedomini/projects/metaclade2/test/pippo/results/1_search pippo
python3 /home/vicedomini/projects/metaclade2/scripts/search_ccms_all.py PF03441 hmmsearch /home/vicedomini/projects/metaclade2/data/models/CCMs/PF03441.hmm.gz /home/vicedomini/projects/metaclade2/test/test.fa /home/vicedomini/projects/metaclade2/test/pippo/temp /home/vicedomini/projects/metaclade2/test/pippo/results/1_search pippo
test/pippo/jobs/1_search/pippo_2.sh 0 → 100644
python3 /home/vicedomini/projects/metaclade2/scripts/search_hmm.py PF00875 hmmsearch /home/vicedomini/projects/metaclade2/data/models/HMMs/PF00875.hmm.gz /home/vicedomini/projects/metaclade2/test/test.fa /home/vicedomini/projects/metaclade2/test/pippo/temp /home/vicedomini/projects/metaclade2/test/pippo/results/1_search pippo
python3 /home/vicedomini/projects/metaclade2/scripts/search_ccms_all.py PF00875 hmmsearch /home/vicedomini/projects/metaclade2/data/models/CCMs/PF00875.hmm.gz /home/vicedomini/projects/metaclade2/test/test.fa /home/vicedomini/projects/metaclade2/test/pippo/temp /home/vicedomini/projects/metaclade2/test/pippo/results/1_search pippo
test/pippo/jobs/1_search/pippo_3.sh 0 → 100644
python3 /home/vicedomini/projects/metaclade2/scripts/search_hmm.py PF03167 hmmsearch /home/vicedomini/projects/metaclade2/data/models/HMMs/PF03167.hmm.gz /home/vicedomini/projects/metaclade2/test/test.fa /home/vicedomini/projects/metaclade2/test/pippo/temp /home/vicedomini/projects/metaclade2/test/pippo/results/1_search pippo
python3 /home/vicedomini/projects/metaclade2/scripts/search_ccms_all.py PF03167 hmmsearch /home/vicedomini/projects/metaclade2/data/models/CCMs/PF03167.hmm.gz /home/vicedomini/projects/metaclade2/test/test.fa /home/vicedomini/projects/metaclade2/test/pippo/temp /home/vicedomini/projects/metaclade2/test/pippo/results/1_search pippo
test/pippo/jobs/1_search/pippo_4.sh 0 → 100644
python3 /home/vicedomini/projects/metaclade2/scripts/search_hmm.py PF12546 hmmsearch /home/vicedomini/projects/metaclade2/data/models/HMMs/PF12546.hmm.gz /home/vicedomini/projects/metaclade2/test/test.fa /home/vicedomini/projects/metaclade2/test/pippo/temp /home/vicedomini/projects/metaclade2/test/pippo/results/1_search pippo
python3 /home/vicedomini/projects/metaclade2/scripts/search_ccms_all.py PF12546 hmmsearch /home/vicedomini/projects/metaclade2/data/models/CCMs/PF12546.hmm.gz /home/vicedomini/projects/metaclade2/test/test.fa /home/vicedomini/projects/metaclade2/test/pippo/temp /home/vicedomini/projects/metaclade2/test/pippo/results/1_search pippo
test/pippo/jobs/2_filter/pippo_1.sh 0 → 100644
python3 /home/vicedomini/projects/metaclade2/scripts/filter_hits.py /home/vicedomini/projects/metaclade2/test/pippo/results/1_search/PF03441/PF03441.hmm.res /home/vicedomini/projects/metaclade2/test/pippo/results/1_search/PF03441/PF03441.ccms.res /home/vicedomini/projects/metaclade2/test/pippo/results/2_filter/PF03441.best.res
test/pippo/jobs/2_filter/pippo_2.sh 0 → 100644
python3 /home/vicedomini/projects/metaclade2/scripts/filter_hits.py /home/vicedomini/projects/metaclade2/test/pippo/results/1_search/PF12546/PF12546.hmm.res /home/vicedomini/projects/metaclade2/test/pippo/results/1_search/PF12546/PF12546.ccms.res /home/vicedomini/projects/metaclade2/test/pippo/results/2_filter/PF12546.best.res
test/pippo/jobs/2_filter/pippo_3.sh 0 → 100644
python3 /home/vicedomini/projects/metaclade2/scripts/filter_hits.py /home/vicedomini/projects/metaclade2/test/pippo/results/1_search/PF00875/PF00875.hmm.res /home/vicedomini/projects/metaclade2/test/pippo/results/1_search/PF00875/PF00875.ccms.res /home/vicedomini/projects/metaclade2/test/pippo/results/2_filter/PF00875.best.res
test/pippo/jobs/2_filter/pippo_4.sh 0 → 100644
python3 /home/vicedomini/projects/metaclade2/scripts/filter_hits.py /home/vicedomini/projects/metaclade2/test/pippo/results/1_search/PF03167/PF03167.hmm.res /home/vicedomini/projects/metaclade2/test/pippo/results/1_search/PF03167/PF03167.ccms.res /home/vicedomini/projects/metaclade2/test/pippo/results/2_filter/PF03167.best.res
test/pippo/jobs/3_arch/pippo.sh 0 → 100644
python3 /home/vicedomini/projects/metaclade2/scripts/simple_arch.py -e 0.001 /home/vicedomini/projects/metaclade2/test/pippo/results/2_filter /home/vicedomini/projects/metaclade2/test/pippo/results/3_arch/pippo.arch.txt
test/pippo/results/1_search/PF03441/PF03441.hmm.res 0 → 100644
HMMer-3 1 199 202 tr|V7B5W0|V7B5W0_PHAVU 283 483 682 2.3e-65 207.5 0.96
HMMer-3 1 200 202 tr|F0RPZ8|F0RPZ8_DEIPM 267 466 757 1.9e-62 198.0 0.95
HMMer-3 1 199 202 tr|A0A072NB93|A0A072NB93_9DEIO 274 469 766 6.9e-56 176.6 0.91
test/test.fa 0 → 100644
>tr|F0RPZ8|F0RPZ8_DEIPM Uracil-DNA glycosylase OS=Deinococcus proteolyticus (strain ATCC 35074 / DSM 20540 / JCM 6276 / NBRC 101906 / NCIMB 13154 / VKM Ac-1939 / CCM 2703 / MRP) OX=693977 GN=ung PE=3 SV=1
MQPVAVVWFKKDLRVSDHAALSRAAERGPVLPLYIYEPEQLGHEEFAGHHLTYLNECLHD
LSARLARLGAPLVIRYGEAVEVLEALSREVTVGSLWAHQETGNGVSFARDLRVHAWARAR
GIPFYEPPQQGVIRRMVNRDGWADAWEERMSAPPLPVPALRGVAGTPASLGVLDHAALRV
PLGRRVIPQGGEAAAHDILESFLQRRGRDYMWAMSSPLTAEDACSRLSAPLAFGTVSART
VLLATRQALARAVAEQDAQWERSLRSFESRLHWRDHFIQRLESEPRMEFENLNRAYDGLR
EPHWNEEYFQRWQEGQTGYPLIDATMRMLRATGWLNFRMRAMLVSFAAQHLWLHWRRPGL
FLARQWLDNEPGIHWSQMQMQSGTVGINRSRIYSPTRQAREQDPDGEFIRRWVPELAGVP
APHIWRPWELPPLAARGLGLRLGRDYPYPVVDEHAPAREAHRRLQAVRDTPLFAAEARRV
YALHGSRKKAVIRAEREKKGLPPRPERPSARRSPLPRRHPMSDQPNLFDTADTQPPVQLP
HDWGAVLHDEISRPSFRRLLEFVEEQRRTATVYPPPEDVFTALRLTSYQDAKVLILGQDP
YHGAGQAHGLAFSVRRGVRVPPSLRNIYQELKEDVGVTPPRHGNLEAWAERGVLLLNAVL
TVREGEPNSHAGQGWEDFTDAVIRALNAKEQRVVFVLWGAYARKKKKLVTAPQHVVIESG
HPSPLSVRHFAGTRPFSAVNRALQEAGEEAVDWSLPQ
>tr|A0A072NB93|A0A072NB93_9DEIO Uracil-DNA glycosylase OS=Deinococcus sp. RL OX=1489678 GN=ung PE=3 SV=1
MPRPLAGPPVQVVWFKKDLRVADHAPLAAAAERGPVLPLYLYEPEQLGHEEFAGHHLTYL
NECLAELDGRLRALGAGLVVRRGEAVAVLEELSELVPMGGLWAHEETGNMVSFQRDRRVR
AWARERGVPFAELPQTGVVRRLRDRDGWADLWEERMSAPVVPVPAALRGTDLPPGGLYTH
AELGVPANDKTIPPGGESVARATLESFLTVRGVNYLREMSSPLTAEESCSRLSAPLAFGT
VSLREVVQATRQRLAAVKGDPDADERWVCSLRSFESRLHWHCHFIQRLESEPQMEVRNLN
RAFDGLRPDAGDPGWNADFFDRWAHGQTGYPLVDACMRMLRETGWLNFRMRAMLVSFASQ
HLWLHWRPTGLFLARQWLDNEPGIHWSQMQMQSSTVGINRVRIYSPTRQAREQDPDGAFI
RRWVPELADVPGDFLHAPWEWSGATRLAYPPPVVDEGKAGAAARARIYAARESEAFETEA
RRVYQKHGSRKKAVLRAERVARGLPAKPVRPPKSAPRRIPPMTDQPGLFGTAPETPKPLI
PAGLPDSWREALHDEFAAPYFHALRDFLVEERRQHTVYPPAPDVFNALRYTPLEAVKVLI
LGQDPYHGPGQAHGLAFSVRPGVRPPPSLANIYKELQADVGFQPPRHGYLRHWAEQGVLL
LNAVLTVRRGEPNSHAGRGWERLTDAVIRQVNAKESRVVFVLWGAYARKKAKLVTNPQHV
ILESAHPSPLSVAKFLGTRPFSKVNAALEESGQTPIDWQLPMEVEE
>tr|V7B5W0|V7B5W0_PHAVU Photolyase/cryptochrome alpha/beta domain-containing protein OS=Phaseolus vulgaris OX=3885 GN=PHAVU_008G173700g PE=4 SV=1
MSGGGCSIVWFRRDLRVEDNPALAAGVRAGAVIAVFIWAPEEEGQYYPGRVSRWWLKQSL
AHLDSSLRSLGTPLITKRSTNSVSSLLEVIKSTGATQLFFNHLYDPLSLVRDHRTKEVLT
AQGITVRSFNSDLLYEPWDVNDAHGQPFTTFSAFWERCLSMPYDPQAPLLPPKRIIPGDA
SRCPCDTLVFEDELEKASNALLSRAWSPGWSNADKALAAFVNGPLIEYSKNRRKADSATT
SFLSPHLHFGEVSVKKVFHLVRIKQVFWANEGNKAGEESVNLFLKSIGLREYSRYISFNH
PYSHERPLLGHLKFFPWVVNEGYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSS
FFVKVLQLPWRWGMKYFWDTLLDADLESDALGWQYISGTLPDGREFDRIDNPQFEGYKCD
PNGEYVRRWLPELARLPTEWIHHPWNAPEYVLQAAGIELGSNYPLPIVGIDAAKVRLQEA
LIQTWQQEAASRAAIENGTEEGLGDSSESAPIAFPQDTLMEERPAEPVRNNPPHGTRRYE
DQMVPSMTSSHVRVEEEETSSDLRNSAADNRAEVPTNVTTQQNARETVNQGELLNVNRNT
RVQNNATMWLRNAAEDSTAESSISTRRERDGGVVPVWSPPASNFSEQYADDENGIGASSS
YLQRQHPQSHQLMNWTRLPQTG
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