I need to use my code with fasta format. Can anybody help?

Question

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

How could I make this work?

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))

Answer 1

One way is to store the header as a separate string from your protein residues. Use a list comprehension to build a list of formatted header-fragment pairs, and then print them to standard output.

#!/usr/bin/env python                                                                                                                                                                                                                                                    

import sys
import re

myprotein = ">jgi|Cormi1|6|CCM_00006m.01\nMSSFTRAIRPALQGGRRVLLAQRLSTPRIAHPIAATALRSLSTTAPRRSVDLSELQPTPI\nTHLSEVETAMADAVSKFATEVVLPKAREMDEAEAMDPAVVEQLFEQGLMGIEIPEEYGGA\nGMNFTAAIIAIEELARADPSVSVLVDVHNTLCNTALMKWGSDALKKKYLPRLATNTVASF\nCLSEPVSGSDAFALATRATETPDGYTITGSKMWITNSMEAGFFIVFANLDPAKGYKGITA\nFVVDKDTPGFSIAKKEKKLGIRASSTCVLNFDDVAVPKENLLGKPGEGYKYAIGILNEGR\nIGIAAQMTGLALGAFENAVRYVWNDRKQFGTLVGEFQGMQHQIAQSYTEIAAARALVYNA\n"

# parse record
my_protein = []
for line in myprotein.split('\n'):
    if not line.startswith('>'):
        my_protein.append(line)
    else:
        header = line

# build sequence
my_pro = ''.join(my_protein)

# cleave sequence                                                                                                                                                                                                                                                        
peptides = re.sub(r'(?<=[^HRK][^P][^R])(?=[FLWY][^P])|(?<=[^HRK][^P][FLWY])(?=.[^P]?)','\n', my_pro)

# build a formatted list
records = ["%s frag.%d\n%s\n" % (header, idx + 1, fragment) for idx, fragment in enumerate(peptides.split('\n'))]

# print list
for record in records:
    sys.stdout.write("%s" % (record))

This gives:

>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
...
>jgi|Cormi1|6|CCM_00006m.01 frag.89
LV
>jgi|Cormi1|6|CCM_00006m.01 frag.90
Y
>jgi|Cormi1|6|CCM_00006m.01 frag.91
NA

---

If you have multiple records in one file called seqs.fa, then you could use standard input to this script (e.g., named digest.py) to process them all at once:

#!/usr/bin/env python                                                                                                                                                                                                                                                    

import sys
import re

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))

Creating a function called digest lets you change the digestion rules in one place. It reduces code bloat and also reduces errors from changing things in one place and not another.

You could use this script like so:

$ ./digest.py < seqs.fa > seqs.digested.fa

The file seqs.digested.fa would look like:

$ cat seqs.digested.fa
>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
...
>jgi|Cormi1|100|CCM_00100m.01 frag.143
PTKTEVRERVRL
>jgi|Cormi1|100|CCM_00100m.01 frag.144
THMHKKEERRTRGDEHE
>jgi|Cormi1|100|CCM_00100m.01 frag.145
W*