====CARD 抗性基因数据库注释====


=== 使用 Transdecoder 进行cds 预测获得氨基酸序列===

说明： 若项目中或者老师已提供氨基酸序列可跳过此步骤

脚本路径：

/PUBLIC/source/RNA/metatr/TRINITY/Transdecoder-ORFs.py

usage :

<code>
 python /PUBLIC/source/RNA/metatr/TRINITY/Transdecoder-ORFs.py --outdir 输出绝对路径 --unigene unigene.fa （fasta 序列名称）
</code>

输出文件格式如下： 注意需要将ID 中 “|” 后 的部分去掉 ** AWK -F '|' '{print $1}' file.pep > out.pep**

<code>
>c50497_g1|m.9 c50497_g1|g.9  ORF c50497_g1|g.9 c50497_g1|m.9 type:3prime_partial len:154 (-) c50497_g1
MDPLTLGGLVALATILVLFSGVSVAVGLLIVSAGFLIVFDGMRSLELMPEILFGKLDNFA
LLSIPMFIIMGASIASTRAGADLYEALERWLTRVPGGLVISNLGACALFSAMSGSSPATC
AAIGKMGIPEMRKRGYPDGIAAGSIAAGGTLGI
>c50497_g1|m.10 c50497_g1|g.10  ORF c50497_g1|g.10 c50497_g1|m.10 type:complete len:140 (+) c50497_g1:2
MEAPMMMNIGIDSSAKLSSLPNRISGISSSDRIPSNTIRKPADTISRPTATETPENSTRM
VASATSPPSVSGSISRPPVRRVCRCAAQAPRNRPPIAAAAARARAAETGRGSRVLVPRRC
QTASRVPRRSARTRIRRIA*
</code>

使用输出的*transdecoder.pep 文件进行后续分析


===使用第一步预测的蛋白序列进行CARD 数据库注释===

<code>
/PUBLIC/software/MICRO/CONCOCT-0.4.0/conda/miniconda2/bin/python2.7 /PUBLIC/source/RNA/metatr/pipline/lib/04.Function/lib/CARD/bin/../softwareRGI/release-rgi-v3.1.1/rgi.py --inType protein -i unigene.pep.fasta --out_file Unigenes.protein.rgi --data wgs --orf 1 --clean 1 --verbose 1 --exclude_loose 1
/PUBLIC/software/MICRO/CONCOCT-0.4.0/conda/miniconda2/bin/python2.7 /PUBLIC/source/RNA/metatr/pipline/lib/04.Function/lib/CARD/bin/../softwareRGI/release-rgi-v3.1.1/convertJsonToTSV.py -i Unigenes.protein.rgi.json -o Unigenes.protein.rgi -x 1
rm app.log
perl /PUBLIC/source/RNA/metatr/pipline/lib/04.Function/lib/CARD/bin/../lib/rgi_DEL.pl Unigenes.protein.rgi.txt Unigenes.protein.rgi.del.txt
</code>


结果说明：

<code>
ORF_ID	CUT_OFF	PASS_EVALUE	Best_Hit_evalue	Best_Hit_ARO	Best_Identities	ARO	ARO_name      Model_type	SNP	AR0_category	bit_score	Predicted_Protein	CARD_Protein_Sequence LABEL	ID
c55570_g8	Strict	1e-30	2.36716e-40	MexV	0.3258064516129032	ARO:3003030, ARO:3000795, ARO:3003055, ARO:3000774	MexV, smeD, adeA, mdtE	protein homolog model	n/a	efflux pump complex or subunit conferring antibiotic resistance	144.821, 125.561, 130.183, 119.013	MTINRAKIIAVVSIFILFIFYGCKGSSGKEQDKKGRGRPPIAVEAFIARTENITSTVNASGTLLSNEEVEIKPELQARVVKINFKEGAKVSKGQLLVKLDDADIAAQLKKVRAQKLLAKKNADRLEQLLKIDGVSKQEYDAAQTQLTAYDADIEALETQLRKTEIRAPFSGTIGLTDISEGAFVTPQNIISTLQQTDPLKVDFSIPEKYTLLLTDEKELSFTIDGLRDTFTAKVYAKEPKVDPMTRSVKVRGRCENKDGVLVPGMFANVQLAIQSRKDAVMVPTESLIPVARGKNIAISRGDKVDIVPVETGLRNEDLVEILKGVQAGDTVITTGLMQLRPNSKVKLTKIEK*	MLLRRMLIMLAAVIAVVAILAGYKVYSIRQQIALFSAPKPPISVTASLAEKRPWQSRLPAIGSLKAFQGVTLTAEVSGTVRDVLFLSGDQVKLDQPLIQLESDVEEATLRTAEADLGLARAEYQRGRELIGSKAISKSEFDRLAAQWAKTSATVAELKAALAKKRVLAPFAGTIGIRQVDVGDYVSPGTPIATLQDLSTLLLDFHLPEQDFPLLSRGQLVKVRVAAYPAQVFDAEIAAINPKVDNETRNLQVRAALENPDGKLLPGMFANLEVMLPGEEQRVVVPETAITFTLYGDSIYVVGQKKDEQGQVSKDDKGQPQQVVERRFVRIGERREGLAVVLEGLEGGEQVVTSGQLKLDNGAAVAIVAERDLQQEH	c55570_g8	gnl|BL_ORD_ID|375|hsp_num:0
c22256_g1	Strict	1e-30	8.27345e-91	Ureaplasma urealyticum  gyrB conferring resistance to fluoroquinolone	0.3212669683257919	ARO:3003305, ARO:3003318	Ureaplasma urealyticum  gyrB conferring resistance to fluoroquinolone, Streptomyces rishiriensis parY mutant conferring resistance to aminocoumarin	protein variant model, protein homolog model	P462S, n/a	antibiotic resistant gene variant or mutant, determinant of aminocoumarin resistance, determinant of fluoroquinolone resistance, gene involved in self-resistance to antibiotic	295.049, 229.18	MLMATSNYTEDNIRSLDWREHIRLRPGMYIGKLGDGASADDGIYILLKEVLDNSIDEYVMGFGKVIDIHINDDGVVIRDYGRGIPLGKVVDCVSKINTGGKYDSKAFKKSVGLNGVGTKAVNALSDFFQVKSVRDGKEKVAEFERGELLKDYKPKKSKEENGTMVFFHPDSSVFKNFKYRKEYVENQLWNYAYLNAGLKLRFNGETFVSRNGLLDLLERKTKSETLRYPIIHFRDEDIEFAMSHGNHYGEQYYSFVNGQNTTQGGTHLNAFKEGVVNAVQGYFSRNNKKFERKDILSSIMAAISVRIEEPVFESQTKTKLGSTDVGPKGPSVRKFINDFVGQKLENFLYRNEEIARALEKRIMQSERERKEIAGIKKLANKRAKKANLHNKKLRDCRVHFCDSSRKTNEEDRKKTTLFITEGDSASGSITKARDVQSQAVFSLRGKPLNCFSLTKKVVYENEEFNLLQHALNIEDGIEDLRYNRVVIATDADVDGMHIRLLLLTFFLQFFPDLVRNGHLYILETPLFRVRDKKQKFYCYNEAEKQEAIKKLRGKAEITRFKGLGEISPDEFGEFIGEDIRLEPVVLDEHTDIDQVLTYYMGKNTPTRQEFIIDNLRVEKDEVEEEDEEVLAIAPEPTEPAEA*     MNDSNKENKYTAESIKVLEGLEAVRKRPGMYIGSTQSEGLHHMIWEIVDNSIDEAMGGFATVVKVIIKKDGVIRVEDDGRGIPVGIHEKTGLSGVETVLTVLHAGGKFDNDSYKVSGGLHGVGASVVNALSKNFKVWVNKNYVQHYVEFINGGHAIEPLKIINDKDIKEKGTTIEFIPDFEIMEENEWDELKIMARLKQLAYLNKGVNIEFESEMTNRKEKWHYEGGLKEYIADLNAEKEPLFDAIVYGEEEKEVKVPGHNDQTYNIKCEVAFQYNNSYNNSTHSFCNNINTTEGGTHEEGFKLAITRLLNKYAIDKKYLKDTDDKITKEDVSEGLTAIISIKHPNPQYEGQTKKKLGNSEVRPYVNEITSIIFEKFLNENPEESKKIVAKVMQAAEARRRSHEAREATRRKSPFESNSLPGKLADCSNRDSSVTEIYIVEGDSAGGSAKTGREREFQAILPLRGKIINVEKAKIDKIFANEEIQNMITAFGAGIGPEFNIEKLRYSKIIIMTDADVDGSHIRILLLTFFYRYMLPLIQNGNVYIAQPPLYKVSYGKTIKYAYSDQELEKIKSTLLNTKYNIQRYKGLGEMNPDQLWETTMDPKNRLLLKVNIEDAAIADKTFSLLMGDDVTPRKEFIEKNAKYVKNIDA	c22256_g1	gnl|BL_ORD_ID|182|hsp_num:0
c52543_g1	Strict	1e-30	0.0	Bifidobacteria intrinsic ileS conferring resistance to mupirocin	0.4641235240690282	ARO:3003730	Bifidobacteria intrinsic ileS conferring resistance to mupirocin	protein homolog model	n/a	antibiotic resistant gene variant or mutant, determinant of mupirocin resistance	931.398	MVGREFIRGRPGREVDRALTGQGLVELLRNDRQQRRTDARRLHQHGVERVESGVLGRLILSAPEARPRTADIPVGQRIEVGHRLARGLRDVIGIQRRTHLLGQLARLGQDVEIQRIVCGRNQLRRALLQIGVEREEGIGVEQRRNRFALNAGDLAAFLGHQQVAAIQNRRADQEPAHDVGAKLVKEAERIRIIAQAFGQLLAVLVQHNAVADRILERRAIKQHRGQHHQGVEPAARLGDIFHDEVSREVLLELFLVFKRIVDLRVGHGA*	MSETTNSHVYPKANEGGETASVAPNPSFPNMEETVLKYWDKDDTFNKSVERNPSGDHSQNEFVFFDGPPFANGLPHYGHLLTGYAKDVIPRYQTMKGRKVNRVFGWDTHGLPAELEAQKELGIDSVDQIEKMGIDKFNDACRASVLKYTHEWQDYVHRQARWVDFEHGYKTLNIPYMESVMWAFKQLYEKGLAYQGYRVLPYCPKDQTPLSAHELRMDADVYQDRQDTTVSVAVKLRDEEDAYAVFWTTTPWTVPTNFAIVVGADIDYVEVRPTQGKYAGKKFYFGKPLLSKYEKELGEDYEVVRELKGSEMAGWRYWPVFPYFAGDKAESEGNVPGPEGYQIFTADYVDTVEGTGLVHQAPYGEDDMNTLNAHGIKSTDVLDAGCRFTAQCPDYEGMYVFDANKPILRNLRNGDGPLAEIPAEHRAILFQEKSYVHSYPHCWRCATPLIYKPVSSWFVSVTKIKPRLLELNQQINWIPENVKDGQFGKWLANARDWSISRNRFWGSPIPVWVSDDPKYPRVDVYGSLEELKADFGDYPRDKDGNVNMHRPWIDNLTRVNPDDPTGKSHMHRISDVLDCWFESGSMSFAQFHYPFENKEKFEQHFPADYIVEYIGQTRGWFYLLHVMATALFDRPAFKNVICHGIVLGSDGQKMSKHLRNYPDVNGVFDKYGSDAMRWFLMSSPILRGGNLIVTAEGIRDTVRQVMLPVWSSYYFFTLYANAANGGAGFDARQLRADEVAGLPEMDRYLLARTRRLVERVEKSLDEFAISDACDAASDFIDVLTNWYIRNTRDRFWKEDVNAFNTLYTVLEVFMRVLAPLAPMESESVWRGLTGGESVHLADWPYVADEKTGEATELGRVLVDDPALVDAMEKVREIVSGALSLRKAAQIRVRQPLAKLTVVVEDVDAVKAYDEILKSELNIKDIEFCTMEDAGSQGLKIVHELKVNARAAGPRLGKQVQFAIKASKTGAWHVDAATGAPVVETPNGEVALEAGEYELINRVEEENAAEADASVSAALPTGGFVILDTVLTADLEAEGYARDVIRAVQDARKAADLDIADRIALVLTVPSANVADVERFRDLIAHETLATSFAVKEGAELGVEVAKA	c52543_g1     gnl|BL_ORD_ID|223|hsp_num:0
c162100_g1	Strict	1e-30	1.86664e-33	mexN	0.26095238095238094	ARO:3003705	mexN  protein homolog model	n/a	efflux pump complex or subunit conferring antibiotic resistance	131.72TIQRESKPDDVRLRTQGQPAVELALYRAKNEDALEMAEVMQRYLQSKRQQLPPNVKLLIYDEQYKPIEERITLLLKNGASGLVLIVAILYLFLSGRVAFWVTVGIPVSFLATLCVLYASGGSINMISLFAMIMALGIIVDDAIVVGEDAAAHYDAGEQALEAAEGGAIRMFWPVVSSSATTIAAFLPLMLIGDYIGAILKAIPWVVMCVIIASLIESFLILPGHLRHSLKGLRDKPVSRWRQGFDQAFEYVREGLFRRLVRSALHNRRVVLAASVAAMLLTVGLLAGGRVKFEFFPTPELDVLIANVGFAAGAPEEDLDAFLSQLETSLEELNQDLGGDFVIAAVTRLGMGVTPGTNFTRSGRQYAHMQVQIRPSDSREIRNAEFIERWKQRIELPPGLDTFGVFEPSIGPPGRDVELRVTGTDLSAVKSVALELGEILRQTAGVNGVDDDTPFGREQILYTPNAQAQVLGLDTSSLGQQLRAALDGELAQIFQDDGSEVEVRVRLMAGDADSILALRDLPILTPGG	MTPRAGISGWCVRHPIATALLTLASLLLGLLAFLRLGVAPLPEADFPTIQINALLPGGSPETMASSVATPLEVQFSAIPGITEMTSSSALGTTTLTLQFSLDKSIDVAAQEVQAAINAAAGRLPVDMPNLPTWRKVNPADSPIMILRVNSEMMPLIELSDYAETILARQLSQVNGVGQIFVVGQQRPAIRIQAQPEKLAAYQLTLADLRQSLQSASVNLAKGALYGEGRVSTLAANDQLFNASDYDDLVVAYRQGAPVFLKDVARIVSAPEDDYVQAWPNGVPGVALVILRQPGANIVDTADAIQAALPRLREMLPATIEVDVLNDRTRTIRSSLHEVELTLLLTIGLVVLVMGLFLRQLSATLIVATVLAVSLSASFAAMYVLGFTLNNLTLVALIIAVGFIVDDAIVVVENIHRHLEAGASKVEAALKGAAEIGFTVISISFSLIAAFIPLLFMGGIVGRLFREFAVSVTVAILISVVASLTLAPMLASRFMPALRHAEAPRKGFAEWLTGGYERGLRWALGHQRLMLVGFAFTVLVAVAGYVGIPKGFFPLQDTAFVIGTSQAAEDISYDDMVAKHRQLAEIIASDPAVQSYNHAVGVTGGSQSLANGRFWIVLKDRGERDVSVGEFIDRLRPQLAKVPGIMLYLRAAQDINLSSGPSRTQYQYALRSSDSTQLALWAQRLTERLKQVPGLMDVSNDLQVGASVTALDIDRVAAARFGLSAEDVSQTLYDAFGQRQVGEYQTEVNQYKVVLELDARQRGRAESLDWFYLRSPLSGEMVPLSAIAKVAAPRSGPLQINHNGMFPAVNLSFNLAAGVSLGEAVQAVQRAQEEIGMPSTIIGVFQGAAQAFQSSLASQPLLILAALIAVYIILGVLYESFVHPLTILSTLPSAGIGAVFLLWAWGQDFSIMALIGIVLLIGIVKKNGILMVDFAIVAQREQGMSAEQAIYQACLTRFRPIMMTTLAALLGAIPLMIGFGTGSELRQPLGIAVVGGLLVSQVLTLFSTPVVYLALERLFHRRGTTTSDGGTAGATAT	c162100_g1	gnl|BL_ORD_ID|516|hsp_num:0
</code>