I need some help. I have written a program that simulates protein cleavage but I need to modify it so that it produces fasta formatted output.
here is all of my sequence in .fas file
>jgi|Cormi1|6|CCM_00006m.01
MSSFTRAIRPALQGGRRVLLAQRLSTPRIAHPIAATALRSLSTTAPRRSVDLSELQPTPI
THLSEVETAMADAVSKFATEVVLPKAREMDEAEAMDPAVVEQLFEQGLMGIEIPEEYGGA
GMNFTAAIIAIEELARADPSVSVLVDVHNTLCNTALMKWGSDALKKKYLPRLATNTVASF
CLSEPVSGSDAFALATRATETPDGYTITGSKMWITNSMEAGFFIVFANLDPAKGYKGITA
FVVDKDTPGFSIAKKEKKLGIRASSTCVLNFDDVAVPKENLLGKPGEGYKYAIGILNEGR
IGIAAQMTGLALGAFENAVRYVWNDRKQFGTLVGEFQGMQHQIAQSYTEIAAARALVYNA
ARKKEAGEDFVRDAAMAKLYASQVAGRVAGLAVEWMGGMGFVREGLAEKYWRDSKIGAIY
EGTSNIQLNTIAKLLQKEYTA*
>jgi|Cormi1|8|CCM_00008m.01
MLAGSNARILRYIVVAGIILIFFYHFSGSRYDTLPRPVPAPDHAQAASQPSPPNDEATTA
GRPVDSTQKSIPADRDRPNSGFPKSVSASTDAAASTLADIDPGPRANATFVSLARNADVW
DIARSIRQVEDRFNRRFNYDWVFLNDKPFDDNFRNITSALVSGTARFGQIPVEHWSVPDW
IDEDKATKVREDMKERKIIYGDSMSYRHMCRFESGFFFQHPIMKNYDFYWRVEPSIELFC
DIAQDPFRFMKENGKKYSFTISLLEYVDTIPTLWDSAVKFIENYPQHVAADNSMEFLSDD
GGQTYNMCHFWSNFEIGSLEWMRSDAYVDFFNSLDQDGGFFYERWGDAPVHSIAAGLLLN
KTELHFFDEIAYFHMPFTHCPNDVQSRIDLKCHCNPKDNFDWSRYSCTSRYFEMMGMQKP
DGVD*
>jgi|Cormi1|10|CCM_00010m.01
MSTSPSDGTVDVDLPDAPTAPFPLHSDTHTANHVENDEDDDPITASYPVFLNPALPLGRR
LLVLQHPNRTDDHGARAPPSELRLKAESGMVEVDMPLDYNEAYDRDKGLRWGRTLQTSMA
AKNGGSHGLAGGFGFGAVQQRGAGAGAGGARKRNEVDAEDLIDWNEAVRQDKVLRTQTLG
GQYPDADEVQYMVGVFQGNDLHLTPVSSLVHLRPQLHHLDAATQQERQAAAKEAGAAAAS
SSGGATAGPGATGNPAARAIHMSIKTTADGETVTTETIADRLRFVQGEAWRKLRYTDENE
EAAWEVYNESLFLSASEARAPPPGSEKKKKTGSNEEELPYRSLQGAVATFASKWESGQLL
EAVSGMKKPPPVVVVPAAVKKAKAAAEAEAKAKDVEEKRKAAEAQMAATATAAAAAEETR
RPKRAPRGGGGLGTAKRPSRAK*
>jgi|Cormi1|11|CCM_00011m.01
MASATTPILPAEGKRNVLITSALPYSNNLPHLGNVIGSVLSADLYARYCRARGYQTLYVC
GTDQYGTATETKALEEGTDPASLCAKYHALHKSIYDWFRIDFDIFDKTPTQHQTDIVQDI
FTKLWKNGYIYEDETIQPFCPVESHNTFLADRFVEGECSICGDKGARGDQCDACGSILDP
LKPEETGAVDGDAAIEVKATGWLVNPRCKVDGTAPEARKTKHLYLKLDDISEELKAWYKT
TADNGWSTNAKAITQSWIDKGLKPRAISRDLKWGVPIPAVEGLNVEDYARKVFYVWFDAC
IGYISITKTYTDGDNRDGKNWEKWWKNPENVELMQFQGKDNVGFHSIVFPSSLLGTKENW
TKVTRISATEYLNYEQGKFSKSRGIGVFGNNAKDTGIDPDIWRFYLLSRRPELADSEFKW
EEFIDVNNNELLKNVGNFIQRTLKFCVAKMDSTVPAATVSNDVIESHKQSANQILASYIE
HQEANKMRIGISDILTFSALGNKFLQDNGLNNKLLAEEPELCNTVINVAINHVHLLAGLL
YPYMPTTAESIFQQLGQEPNPFIPDVFGFTAVPVGHKIGTPGPLFSVIPAAKLDEWRDAY
GGAELKKQKAIEAEKAAAKKAKKLADKEKKKAKKAETADLKTEGASTAADISKLSLEEKK
*
>jgi|Cormi1|15|CCM_00015m.01
MAEEEVRSTVALVVGALLPALMTVFFNGLPGAVGGSNLPRWGVRLPILLTCAAQLWFMLV
SRVVPEPYLDEIFHIPQAQKYCEGRFFDWDDKITTPPGLYFFSVAVHRIASALRIPQLSV
CDPFSLRAVNFAGVLVVSYLALWCRQALEARQHEAISSPTPARVRAFSQYAVHTAVNIGL
FPLLFFFGGLYYTDVLSTGVVLAAFLNHLRRVGVPRSSVWSDLGTVALGVAALGMRQTNV
FWIVVFMGGLEAVHAVKTLRPARVDQPVMTTLAAQCRYFAWRYSLGDIHDLPVHKAYPDD
MIFTALSIGIAALCNPLRVVRQIWPYLAVLASFAAFVQWNGSVVLGDKSNHVATIHLAQM
LYIWPFFAFFSLPLLLPSGLSFLNMVVSFFRTHARASPTPDAAADGLLRATLRFFHSKVL
WPAYLAATAVLSLAVVRFNTIIHPFTLADNRHYMFYVFRYTIRRGGAVRLALALPYTVCR
WVVWDALGGHNSWSLGNDKPTAFVSHPFWTPPSAKVRRQTSTSYPRPPERASTAESRQAS
EAALKARLEQDSLYLSQQSVSTSTGLIFLLATALSLVTAPLVEPRYFILPWVVWRLMVPA
WRLQDHLRGGILEGSPAAKAVAHWSASYDLRLFLESAWHVVINLATGYVFLYKPYVWRAE
DGTVLEGGNLQRFMW*
>jgi|Cormi1|20|CCM_00020m.01
MTNTIVIVGQVLFPLLTRTTNCIANERRPPSSGGVSGLTSAYLLSKSKGNTVTLVAKHMP
GDYDIEYASPIAGANVLPMNPDADSRWERRTWPEFVWLCRNVPEAGFHFKNALVLRQHKD
QEADPSGGPIDPLFDRDPWYRHLTPDYRELAASELPPGQDSGCSFTSMCLNTPMYLFWLV
GQCLRQGVVFRRAVLHDLTEARRLAYSGRPADVLINATGLGARTLGGVRDAGMLPARGQI
VLVRNDGSSMLNTSAVDDGSGEILYTMQRAAGGGTILGGTYDLGNWESQPCPNVATRIMA
RAVRLDPALAGGKGVAGLDVIRHAVGLRPYRKGGVRVERETLRDEVDGASVHVVHNYGHA
GWGFQGSFGCAEKVVELVNEIRAANGEDLSKEPTLFNFEAAAASKL*
>jgi|Cormi1|21|CCM_00021m.01
MEATNSPARAAREPAVHVRALTFVVDVACGRHALSPLIPVALWLADAVLTCLIIWKIPYT
EIDWVAYMEQITQFVHGERDYTKIKGGTGPLVYPAAHVYTYTGLYYLTGEGENVLLAQQL
FAVLYMVTLGLVMLCYWKAKVPPYIFPLLILSKRLHSVFVLRCFNDCFAVFFLWLAIYSF
QRRLWALGSMAYTWGLGIKMSLLLVLPAVGAVLLHACGFSGALSLAWLMAQVQIVIALPF
IATNTNGYLARAFELSRQFQFEWTVNWRMLGEATFRRREWALLLLGLHAATLALFLATRW
MRPAGKTLRRMVPAWLRGRAALTPDEEIRVSRRVTPDFVLTTMLSANLVGLLFARSLHYQ
FYAYLAWSTPFLLWRALPGGAAVLTYPLWLLQEWAWNVFPSTSESSTAAVAVMATTVLVV
YFGTRNDGLTIKKPAAKKQ*
>jgi|Cormi1|32|CCM_00032m.01
MRLIAAQMLRGTAQRRGFATTPRRLDNYAFVGLGQMGYQMAKNLQSKLQPSDKISLYDIN
TDAMKRLQVEMKAASNGAAVELAASAHDAAKEADTVITVLPEPQHVQGVYKSILTPSLPR
RDRVFIDCSTIDPSTSRAVAASVAAAQQGAFVDAPMSGGVVGATAGTLTFMLGAPASLLP
RLEPALLTMGRKVLHCGDQGAGLSAKLANNYLLALNNIATAEAMNLGIRWGLDPKKLAGV
LNVSTGRCWPSEVNNPVKGVVETAPAGRDYSGGFGIALMKKDLRLAMVAAAEAGADMKLA
DAAFKVYEEASEREDCKGRDFSVVYRYLGGKE*
>jgi|Cormi1|35|CCM_00035m.01
MPGLPTSVDLDECISRLYKKELLAESVIEAICAKTKELLMRESNVVHVQAPVTVVGDIHG
QFYDLIEIFRIGGYCPDTNYLFLGDYVDRGMFSVETISLLVCLKLRYPERVHLIRGNHES
RGVTQSYGFYTECSRKYGNANVWHYFTDMFDFMTLSVVIDNQIFCVHGGLSPSIHSIDQI
KIIDRFREIPHEGPMADLVWSDPDPDRDEFSLSPRGAGYTFGAQVVKKFLAVNNMSHILR
AHQLCQEGFQVLYEDRLSTVWSAPNYCYRCGNMASVLEVNSDGERFFNVFAAAPENDQVK
DMQPGIDKAGDGNALPDYFL*
>jgi|Cormi1|37|CCM_00037m.01
MRYAFAYAALVSTASAHGLVTMIKGDNGVMMPGLGVTDGTPRDCSSNGCGSQADTSIIRN
RDMQQNPLGKTQGTGPVDAAVNVAAFMGTSKNAPKNNGASAGVGQEDDLSGLPAGAAKRH
EERKNMVRGLFGDLLGGAAGGAGAAGGAAGGAAGGLGGLLGGAGGAGGAAGGAAGGLGGL
LGGLGGGGGGTKSNLAAESMVADTAGMGSTQGMPTSDSTGTVSLVYRQINQDGAGPLTAA
VDGTSGGTDASAFQQAEVTKDVPGLGIGGLSLATNTDFPLQVKMPAGMTCEGTVGGVKNV
CIVRVRNSAAAGPFGGSAAFTQNATARKRAIAYRLRKRMEIAREAVPQIDYTKADAAEEL
EDEEDE*
>jgi|Cormi1|65|CCM_00065m.01
MRWHVYWGVVQLVELSNVDKRVAVACHVHTLALPDISLSHHPASSATVTPVIIVRLNRPE
SRHAYTDTMGASLVTAYGLLSADPRVRAIVLTSADASNKFFCAGMDFNVRAQRVEDPLQY
RDSGGTVSIAMHRCQKPIVAAVNGAAVGIGMTMTLPATVRVASTKAKCGFVFAQRGFCME
ACSSFFLPRLIGTAKAMHLVSTGAVYPATHRLFDDLFSEVVEPEDVLPTALKIAEGMAQN
CSIVSTQVMKDMMYSGPKSPEEAHLLESKIFYSLTCPDTDSAEGVQSFLQKRPPKFTGTM
ENQRPFGWPWWSNLDVRPKI*
>jgi|Cormi1|71|CCM_00071m.01
MSRIEKLSISGVRSFSPACREAIQFNTPLTLIVGYNGSGKTTIIECLKYATTGELPPNSK
GGAFIHDPKLCGEKEVLAQVKLQFRSINDRQHVATRSLQLTVKKTTRSQKTLDCSLVVLN
NGEKTTTSTRQAQLDEMIPERLGVSPAILDAVIFCHQDESLWPLSEPSVLKKRFDEIFEA
LKYTKAIENLKVLRKKQVEELGKLQNDEFHNKGNKDRGDRAEKRMTGLQAEIEAAREKCE
AITAHMQETQDKIKQKHEQANSFLQIVQNLGNKREQLDYRQDAVDELRQTIDELPEDDRS
LERQLVQYEESMRRQSEEAQRNKTQYGDLQQDLVKSRKSLSTKLAEQGKHQSDKEKHERQ
LKMRMEMVQEAAQHHGFRGYEDDLTDALIKQFNDKIQKLFAEKKRELERLQKENAAELDK
ASATISEFEGQKAARTQDRVSAKQRQGAIEKRTIVLQNEASSIDVDEGLKAILDGQLGEL
ESKFSQVHREFETAAWDNQISDENAKLWQLESESEKLGRELIECTRLASERAQLDFRRKE
LSDRKLKLTSLTETWRSKLDKVIGGDWSPEDLEAKFQALLAAQNKALQEARQQQEQTRQK
QARVDFKLKTVKETCEQKQTDQIECKKKVLQALQNVRDSAVIEDYTEEVSATEQQIETLR
DDLSLIDALKDYYTKCKRALDAKKTCLLCDRHFDDSQAASIDRLRVKIDRHLNSKTKIEA
EQDLSEASSTLQSLVAVRSQYDTYERLGKELPGLRDERKSIEADHESTERLLEEHDAVVA
AEEDKKRDMNDMSKTVSNITQTLREIKDSEGQVERIASQQQSVGTGRSADEIHDLQGTVS
EQMRASKNRVAKLSNDRQRARDQISTLELEKSELRNKISLTLGQLDKKQDLLGQIQSLKE
EQTHQREAIQRADEELEKVEPRITEARSIRDETLKRGRAKEQVVTESRDSVATSINEIKM
IESDIRDYEDRGGASNLASNQRAIATLEQNITTTETEISELTQRTNKLKQDIDNGDRTKK
NINDNLNYRKHLRMLETLRGEINELEDRNAHEDYERLQGEARALENQSNRLFAERGSVMG
SMKTKDEDLDRLLKEWEMDYKDAKQKYRESHIRVETTKAAIEDLAQCGAAVDKAVMQFHA
MKMAEVNRIAGELWQSTYQGTDIDTILIRSDNEGTTGRRNYNYRLCMVKQDAEMDMRGRC
SAGQKVLASIIVRLALAESFGVNCGLIALDEPTTNLDRDNIKSLAESLHNIIRTRQAQSN
FQLIVITHDEDFLRHMRCSDFCDSFFRVKRDDKQNSVISRESITKIF*
>jgi|Cormi1|75|CCM_00075m.01
MPSSTPLPPPKGFLSYPDVEEIISPRYEPRKDANPVLSGLPLVIASSLLTHSSFLAKIFY
NNAGLQKIKDLPFLDDVPYTFHPLVIPLGDNGPMVELGEAQLNPKNRGDTHHYTASDYHA
MYKSGQVTPLQVTETLLSITSKYAKEASIYQDAWADSHGADQLALDAAKASTERWAAGKA
LGVLDGVPIGVKDDLSVKGYIDHDGMAYKKGVPFFKSAEETVWPVQALQAAGAVVIGKNR
MHELGSDTNGLNPHQGTPTNHLNNQYYPGGSSSGAGSSLGAGVIPIAVGTDAGGSVRFPA
VYNGVYGLKPTHHRTLEMNSTMCVAGPMAANVADLTIAYRIMSQPDPTTSIQSRFAVSQP
PAAGTNKYIGVDRAWWGASDPRVIGACNKALEYFTSQGYELVDITIPYIDEAQTAHGGVT
IAEMTEAARRRGGDKTSWTTLIGPVNKLVLALGLETNAADLLKFNSMRTLIMRHMAWLFQ
KYPGLLILTPTAPFLGWEKKPAHAKYGVSDGDKTFLSMIYVFLANIAGLPALTAPIAYVD
PDQGEGKVCIGMMATGEWGAEEALLAWAADAETYLHEVYPEGRRRPKTWVDVLGLAAKQG
TV*
>jgi|Cormi1|77|CCM_00077m.01
MLSSTITRSRPTATMAKLAGGMLVAGLATKYTIGVAHAESPAAPPRSQVFGRGPALVSLV
LEDAEMVNHNTRRLRFRFQDKEAASGLPLTSALLTYSWPKDSWLPVIRPYTPITTADETG
HLDLLVKQYPNGKSSTHLHSLKPGHTLFFVAPLSGHQWQPNSYKHVTLIAGGAGITPIYQ
LAQGILNNPDDKTAVTVVFGVNSDRDVLFKKEFDEYEQRFPGRFRAVYTVSSPVPGSPHR
KGHVNEALLKEVTPAPGPGNMVFVSGPPPMETALVGSRREPGILEKYGYRKEQVYKF*
>jgi|Cormi1|78|CCM_00078m.01
MAADASFDNLARQFSHLPLIDKLPNCFPDINPVDIYRAHITSILSHITGADKSLIYPVLQ
WTATLDKGDLMLAIPALRIKGKPDDLGKQWVEKWPESPLVEKPVHNGAFISFFFKPEPMA
KTVIPMALQHKQDFGSNPANGLRDQNDPSKGRQKIVIEFSSPNIAKPFHAGHLRSTIIGG
FLANLYRSAGWDVATVNYLGDWGKQYGVLALGFEKYGSEEELVKDPINHLFTVYVKISKE
VAEEKEQADKLKAEGKEEEAQKILDNGVDEKARSYFKKMTEGDEQAIALWKRFRDYSIER
YKQTYARLNIHFDEYSGESKVSEDEMQQAAAKLKEMGLAHEDRGALLMDFTKSVPGKEGK
TLGKAILRKKDGTALYLTRDISELINRHERYKFDKMIYVIASEQDLHVKQFFKIVRMMGR
DDIADKCQHVNFGLVLGMSTRKGTVKFLNDILRDVGDHMHDVMKKNEDKYSQVEDPEQIA
DKLGISSVMVQDMNGKRINNYTFDLSRMTSFEGDTGPYLQYAHARLCSIYRKAELSDEAI
AAADLSLLTEPMAVNLLRVIAQWPDVVQNVLKTLEPTTILTYLFKLTHTLSTSYTHLRIV
GSEPEVMKARLALYNSTRVVLYNGMAILGLTPIERM*
>jgi|Cormi1|79|CCM_00079m.01
MRSRNASPHIGPWRNPARRVRHGTTRNYFDSGCSVWMSSPSRLSAPVPPASPLQKNKFSH
IAIYEQRAATGGVWNTSHVSQEPGFSIPRTTPTSEHEYVVVEDGHDAGARVELVSPVYDN
LETNIPHGLMSYTDLEFPAGTPLFPEHGTVLAYIQQYGRDVEHLVTFETQVRDVRKTTAE
DGRLGWTVETKDLKSGVVSAKSYDAVVAASGHYSDPFVPDIPGIAEFEAVQPGAILHSKF
YRRPEQFTGKKVVVVGNAASGIDISHQIATSAQLPVLISEKDVPGAPPAASNNWSRHVGQ
IVELLPVTRSVRFSSGRIEDGVDAVIFCTGYHYSFPFLGSLAPGITAPNGTYADHLWEHM
LYAPDPTLALLVIPKRIVPFPFAEAQMAVIARIWAGRLNVPNQSERDAWVRRCGAESAPG
ARHTFGYPQDVDYINRLHALSGQARPDAERGLENDGAGKRSPYWGEELSWVRSQIFAIKV
ASRALGERRKECKTLADLGFDFQAAK*
>jgi|Cormi1|87|CCM_00087m.01
MFLLATLFALSALPWTAPAMRSDHLAKLRQETVDMFYHGYNNYMLHAFPEDELRPVSCQP
LTRNPNKPADIGLNDVLGNYSLTLIDSLSTLAILAGGPANEKYTGSQALSDFQDSVAQFV
SYYGDGRQGSSGQGLRSRGFDLDSKVQVFETVIRGVGGLLSAHLFAVGDLPIRGYDPKPD
SKWASEDPLETAPISWHGGFRYDGQLLRLALDLSERLLPAFYTKTGIPYPRVNLRSGIPF
YINSPLHQDSEDTEPVVGNAEITETCSAGAGSLTLEFTVLSRLSGDPRFEQAAKRAFWEV
WERRSDIGLIGNGIDAERGVWIGPHSGIGAGMDSFFEYALKSHILLSGQETPNMTRSHRQ
STTGWLDPNSLHPPLPPEMHSSDAFLEAWHQAHASVKRYIYTDRNHFPYYSNNHRATGQP
YTMWIDSLGAFYPGLLALAGEVDEAVEANLVYTALWTRYGAIPERWSVRESNVEPGIAWW
PGRPEFIESTYHIYRATADPWYLRVGEMVLHDIQRRCWVACGWAGLENVLSGEKQDRMES
FFLGETTKYLYLLFDPEHPLNNLDAAYVFTTEGHPLIIPRRARGSSTPRRRASRTSRQEE
KDVAVYSYYDTRFTNSCPAARTPTEPLAGSNTAARRNLFDVSRFTNLYNTPNIHGPLESF
KTRDEHKGIITQYRATSNYSVFPWTLPPTMLPHNGTCPVPSNRILSWIEFPTVDPAPSLF
ATRGGGGDSNTPLRWYHNVGPTVERVDGLKLQLEQEFNEAAGTDVWMVTHVAGKTVGRHE
NVIFHADHVRHFRDDAFSVLRRKDMVEVVLLVQPEPTPQASRELPPAVMPLPVPGALDEV
SSLDAAPDNTSSTRRPSVRASGQPPATDPDSLFKSILRAVSSALEGSATASTPSPSPLRG
SGSGSGSRDDSSNSDDDVGVASIHSWLANTATGAGAFPLPSVRDALLRNSPDFSAADPAA
SLPWRHVYMAGSACDGPLPEDAPRRHQVIVMRRGGCPFGDKLAHVPNFVPDEASLQLVVV
VDEEGGGHVDDAPRPLLATEQRTPRGTPRLHGIPMVLLPASKGTYELFGEAAAVGLRRKY
VVKSQGYVIENAIVM*
>jgi|Cormi1|88|CCM_00088m.01
MSAGHRVARVHLKEKNTAQDASGRQPSSSSSATAQLASAKVVLGNNLRRFPDFPIPGINF
VDIMPLFANPEAHATLLNALELQITQTFVNTKPDVIVGLDARGFLFGPGLALRLGVPFAA
VRKQGKLPGPCVTAEYVKEYGKDFFQMQEDAIREGQKVLVVDDIIATGGSAKAASDLITQ
LKGHVMGYLFILEIPGLNGRDKLGAAPTTILLQDE*
>jgi|Cormi1|96|CCM_00096m.01
MHLVPKELDKLVITQLGLLAQRRLARGVKLNHAEATALIANNIHELIRDGNHTVADLMAL
GATMLGRRHVIPSVCHTLKEIQVEGTFPTGTYLVTVHNPISTNDGDLARALYGSFLPVPR
DADRLFPAALDPADFAPARQPGAVVAVKGDKITLNADRRRIALRVVSEGDRPIQVGSHYH
FIETNPQLVFDRARAYGFRLDIPAGTSYRFEPGDAKTVTLVEIAGHQVIRGGNGLATGGV
ERWRVDAIVERLQKAGYAHAPEPEVNGVVAGRRRAAAARVPRPYRMDRTAYTVMFGPTTG
DRVRLSSTDLWVKVERDYTTYGDECKFGGGKTLREGMGQASGRPDADSLDLVITNALIID
YTGIVKADIGVKNGIIVGIGKAGNPDVMEGVSPNMIVGSCTDVIAGENKIITAGAIDTHI
HLICPQQAQEALASGVTTFLGGGTGPSAGSNATTCTPGKHLMKQMLQACDALPVNVGITA
KGSDSAPEALREQVAAGACGLKIHEDWGATPSAIDTCLSVCDEMDVQCLIHTDTLNESGF
VESTIASFKNRTIHTYHTEGAGGGHAPDIISVVERANVLPSSTNPTRPFTRNTLDEHLDM
LMVCHHLSKDIPEDVAFAESRIRAETIAAEDVLHDTGAISMMSSDSQAMGRCGEVVLRTW
NTAHKNKLQRGCLPEDDGTGADNFRVKRYVSKYTINPALAQGFSHLVGSVEVGKLADLVV
WDPAWFGTKPHQVIKSGLIAWSQMGDPNASIPTVQPVIGRPMFASFVPAASVVFVSQASV
ASGAVASYGLRKRVEAVRGCRTVGKADMRFNDAMPKMRVDPESYTVEADGEVCTAEPAET
LPLTQSWYGILDNQNAPA*
>jgi|Cormi1|100|CCM_00100m.01
MAARLSAAALAPLRPISSSVCAARQLSQSLLQSQQTRGVAQTYLKKVAEGEERWKARAER
IQNGEQRHVWDILDERGYIKDVAGNTDRIKEVMRIKRIGAYVGIDPTADSLHVGHMLPLM
PLFWLWFHGYPAVTLIGGSTARIGDPTGRLQSREHITNSDISKNITKIHYQLSKLWHNVV
QMRIKYGYEDDWAAKRSLLNNNMWLQGLTLYDFIKRLARDTRIGPMLSRDTAKRKLTDGD
GMSLGEFMYPLLQGWDFWHMYNKIGVQMQIGGSDQYGNIVSGIESLKTIRETEEAPYARM
ESGWQHDPIGFTVPLLTDSAGVKFGKSAGNAIWLDEFKTSAFELYGYFMRRTDDEVEKLL
KLFTFLPMPKIQSIMEEHNADPAKRIAQHNLAFEFVSLIHGSQKALEEAQQHSFRFGGEL
PSIVKEPAASSGIINANTAPRSDIKLPRSVMKLSPAKLLFATGLAPSAAEGQRLVKMQGA
YVAAQPGQKRGLVPGNLNWTPMKMWYPEETSKFLLDDRMLILRKGKHNVRIVELVDDEEW
KASGEFYPGEPYTGEVRRRKQEIIAQAAEDGKTLTMTQVNKMLKKKGRQEGLRVANNPDI
ELPTKTEVRERVRLTHMHKKEERRTRGDEHEW*
My current code:
import re
myprotein = ""
my_protein = []
for protein in myprotein:
myprotein = protein.rstrip('\n')
my_protein.append(myprotein)
my_pro = (''.join(my_protein))
#cleaves sequence
peptides = re.sub(r'(?<=[^HRK][^P][^R])(?=[FLWY][^P])|(?<=[^HRK][^P][FLWY])(?=.[^P]?)','\n', my_pro)
print (peptides)
the output is like
MSS
F
TRAIRPAL
QGGRRVLL
AQRL
STPRIAHPIAATA
L
RS
LSTTAPRRSVD
L
SE
L
QPTPITH
L
SEVETAMADAVSK
F
ATEVVL
PKAREMDEAEAMDPAVVEQ
L
F
EQG
L
MGIEIPEE
Y
GGAGMN
F
TAAIIAIEE
L
ARADPSVSV
L
VDVHNTL
CNTA
L
MK
W
GSDA
L
KKKYLPRL
ATNTVAS
F
C
L
SEPVSGSDA
F
A
L
ATRATETPDG
Y
TITGSKM
WITNSMEAG
F
F
IV
F
AN
L
DPAKG
YKGITA
F
VVDKDTPGF
SIAKKEKK
LGIRASSTCV
L
N
F
DDVAVPKENL
L
GKPGEG
Y
K
Y
AIGI
L
NEGRIGIAAQMTG
L
A
L
GA
F
ENAVRY
VW
NDRKQFGT
L
VGE
F
QGMQHQIAQS
Y
TEIAAARA
LV
Y
NAARKKEAGED
F
VRDAAMAK
L
YASQVAGRVAG
L
AVE
W
MGGMG
F
VREGL
AEK
Y
WRDSKIGAI
Y
EGTSNIQ
L
NTIAK
L
LQKE
YTA
I need every sequence on a separate line, starting with the sequence header like:
>jgi|Cormi1|6|CCM_00006m.01 frag.1
MSS
>jgi|Cormi1|6|CCM_00006m.01 frag.2
F
>jgi|Cormi1|6|CCM_00006m.01 frag.3
TRAIRPAL
import sys
import re
sequence = open(input('Enter input filename: '),'r')
def digest(sequence):
return re.sub(r'(?<=[^HRK][^P][^R])(?=[FLWY][^P])|(?<=[^HRK][^P][FLWY])(?=.[^P]?)','\n', sequence)
seq = ""
header = None
for line in sys.stdin:
if not line.startswith('>'):
seq = seq + line.rstrip()
else:
if header:
for idx, fragment in enumerate(digest(seq).split('\n')):
sys.stdout.write("%s frag.%d\n%s\n" % (header, idx + 1, fragment))
seq = ""
header = line.rstrip()
# final pass
for idx, fragment in enumerate(digest(seq).split('\n')):
sys.stdout.write("%s frag.%d\n%s\n" % (header, idx + 1, fragment))