Mercurial > repos > yufei-luo > s_mart
comparison commons/tools/tests/MockFastaForReplaceGreaterThanSymbolInFastaHeader.py @ 18:94ab73e8a190
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
| parents | |
| children |
comparison
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| 17:b0e8584489e6 | 18:94ab73e8a190 |
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| 1 class MockFastaForReplaceGreaterThanSymbolInFastaHeader(object): | |
| 2 def write(self, inFileName): | |
| 3 f = open(inFileName, 'w') | |
| 4 f.write(">sp|P0A2V0|NDVA_AGRT5 Beta-(1-->2)glucan export ATP-binding/permease protein ndvA OS=Agrobacterium tumefaciens (strain C58 / ATCC 33970) GN=ndvA PE=3 SV=1\n") | |
| 5 f.write("MTLFQVYTRALRYLTVHKWRVAVVVIANVILAAITIAEPVLFGRIIDAISSGTNVTPILI\n") | |
| 6 f.write("LWAGFGVFNTVAYVAVAREADRLAHGRRATLLTEAFGRIISMPLSWHHLRGTSNALHTLL\n") | |
| 7 f.write("RASETLFGLWLEFMRTHLATFVALVLLIPTAMAMDLRLSFVLIGLGIVYWFIGKWVMGRT\n") | |
| 8 f.write("KDGQASVEEHYHSVFAHVSDSISNVSVLHSYNRIEAETKALKSFTEKLLSAQYPVLDWWA\n") | |
| 9 f.write("FASALNRTASTVSMMIILVIGTVLVKNGELRVGDVIAFIGFANLLIGRLDQMRQFVTQIF\n") | |
| 10 f.write("EARAKLEDFFVLEDAVKEREEPGDARELSNVSGTVEFRNINFGFANTKQGVHDVSFTAKA\n") | |
| 11 f.write("GETVAIVGPTGAGKTTLINLLQRVYDPDSGQILIDGTDISTVTKNSLRNSIATVFQDAGL\n") | |
| 12 f.write("LNRSIRENIRLGRETATDAEVVEAAAAAAATDFIDSRINGYLTQVGERGNRLSGGERQRI\n") | |
| 13 f.write("AIARAILKNAPILVLDEATSALDVETEARVKAAVDALRKNRTTFIIAHRLSTVRDADLVL\n") | |
| 14 f.write("FLDQGRIIEKGTFDELTQRGGRFTSLLRTSGLLTEDEGQQPRPKAIAS\n") | |
| 15 f.write(">sp|Q694C1|ABC3G_GORGO DNA dC->dU-editing enzyme APOBEC-3G OS=Gorilla gorilla gorilla GN=APOBEC3G PE=2 SV=1\n") | |
| 16 f.write("MTPQFRNTVERMYRDTFSYNFNNRPILSRRNTVWLCYEVKTKDPSRPPLDAKIFRGQVYS\n") | |
| 17 f.write("ELKYHPEMRFFHWFSKWRKLHRDQEYEVTWYISWSPCTKCTRNVATFLAEDPKVTLTIFV\n") | |
| 18 f.write("ARLYYFWDQDYQEALRSLCQKRDGPRATMKIMNYDEFQHCWSKFVYSQRELFEPWNNLPK\n") | |
| 19 f.write("YYMLLHIMLGEILRHSMDPPTFTSNFNNEHWVRGRHETYLCYEVERLHNDTWVLLNQRRG\n") | |
| 20 f.write("FLCNQAPHKHGFLEGRHAELCFLDVIPFWKLDLHQDYRVTCFTSWSPCFSCAQEMAKFIS\n") | |
| 21 f.write("NKKHVSLCIFAARIYDDQGRCQEGLRTLAEAGAKISIMTYSEFKHCWDTFVYHQGCPFQP\n") | |
| 22 f.write("WDGLEEHSQALSGRLQAILQNQGN\n") | |
| 23 f.write(">sp|P0A4M1|ZTOX_ENTFA Zeta-toxin OS=Enterococcus faecalis PE=3 SV=1\n") | |
| 24 f.write("MANITDFTEKQFEDRLEKNVERLTKNRLAVESPTAFLLGGQPGSGKTSLRSAISEETQGN\n") | |
| 25 f.write("VVIIDNDTFKQQHPNFDELVKLYEKDVVKYVTPYSNRMTEAIISRLRDKGYNLVIEGTGR\n") | |
| 26 f.write("TTDVPIQTATMLQAKDYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDI\n") | |
| 27 f.write("VVKNLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISPKETLERELNRKVSGKEIQ\n") | |
| 28 f.write("PTLERIEQKMVQNQHQETPEFKAIQQKMESLQPPTPPIPKTPKLPGI\n") | |
| 29 f.close() | |
| 30 | |
| 31 class MockFastaForReplaceGreaterThanSymbolInFastaHeader_withoutGreaterThan(object): | |
| 32 def write(self, inFileName): | |
| 33 f = open(inFileName, 'w') | |
| 34 f.write(">sp|P0A2V0|NDVA_AGRT5 Beta-(1 to 2)glucan export ATP-binding/permease protein ndvA OS=Agrobacterium tumefaciens (strain C58 / ATCC 33970) GN=ndvA PE=3 SV=1\n") | |
| 35 f.write("MTLFQVYTRALRYLTVHKWRVAVVVIANVILAAITIAEPVLFGRIIDAISSGTNVTPILI\n") | |
| 36 f.write("LWAGFGVFNTVAYVAVAREADRLAHGRRATLLTEAFGRIISMPLSWHHLRGTSNALHTLL\n") | |
| 37 f.write("RASETLFGLWLEFMRTHLATFVALVLLIPTAMAMDLRLSFVLIGLGIVYWFIGKWVMGRT\n") | |
| 38 f.write("KDGQASVEEHYHSVFAHVSDSISNVSVLHSYNRIEAETKALKSFTEKLLSAQYPVLDWWA\n") | |
| 39 f.write("FASALNRTASTVSMMIILVIGTVLVKNGELRVGDVIAFIGFANLLIGRLDQMRQFVTQIF\n") | |
| 40 f.write("EARAKLEDFFVLEDAVKEREEPGDARELSNVSGTVEFRNINFGFANTKQGVHDVSFTAKA\n") | |
| 41 f.write("GETVAIVGPTGAGKTTLINLLQRVYDPDSGQILIDGTDISTVTKNSLRNSIATVFQDAGL\n") | |
| 42 f.write("LNRSIRENIRLGRETATDAEVVEAAAAAAATDFIDSRINGYLTQVGERGNRLSGGERQRI\n") | |
| 43 f.write("AIARAILKNAPILVLDEATSALDVETEARVKAAVDALRKNRTTFIIAHRLSTVRDADLVL\n") | |
| 44 f.write("FLDQGRIIEKGTFDELTQRGGRFTSLLRTSGLLTEDEGQQPRPKAIAS\n") | |
| 45 f.write(">sp|Q694C1|ABC3G_GORGO DNA dC to dU-editing enzyme APOBEC-3G OS=Gorilla gorilla gorilla GN=APOBEC3G PE=2 SV=1\n") | |
| 46 f.write("MTPQFRNTVERMYRDTFSYNFNNRPILSRRNTVWLCYEVKTKDPSRPPLDAKIFRGQVYS\n") | |
| 47 f.write("ELKYHPEMRFFHWFSKWRKLHRDQEYEVTWYISWSPCTKCTRNVATFLAEDPKVTLTIFV\n") | |
| 48 f.write("ARLYYFWDQDYQEALRSLCQKRDGPRATMKIMNYDEFQHCWSKFVYSQRELFEPWNNLPK\n") | |
| 49 f.write("YYMLLHIMLGEILRHSMDPPTFTSNFNNEHWVRGRHETYLCYEVERLHNDTWVLLNQRRG\n") | |
| 50 f.write("FLCNQAPHKHGFLEGRHAELCFLDVIPFWKLDLHQDYRVTCFTSWSPCFSCAQEMAKFIS\n") | |
| 51 f.write("NKKHVSLCIFAARIYDDQGRCQEGLRTLAEAGAKISIMTYSEFKHCWDTFVYHQGCPFQP\n") | |
| 52 f.write("WDGLEEHSQALSGRLQAILQNQGN\n") | |
| 53 f.write(">sp|P0A4M1|ZTOX_ENTFA Zeta-toxin OS=Enterococcus faecalis PE=3 SV=1\n") | |
| 54 f.write("MANITDFTEKQFEDRLEKNVERLTKNRLAVESPTAFLLGGQPGSGKTSLRSAISEETQGN\n") | |
| 55 f.write("VVIIDNDTFKQQHPNFDELVKLYEKDVVKYVTPYSNRMTEAIISRLRDKGYNLVIEGTGR\n") | |
| 56 f.write("TTDVPIQTATMLQAKDYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDI\n") | |
| 57 f.write("VVKNLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISPKETLERELNRKVSGKEIQ\n") | |
| 58 f.write("PTLERIEQKMVQNQHQETPEFKAIQQKMESLQPPTPPIPKTPKLPGI\n") | |
| 59 f.close() |