print('Python version ' + sys.version+"\n\n\n\n")

print("Hi baby, welcome to SynBioCAD. \tI'm here for you.")

print("Right now, we assume you're working in S. cerevisiae.\n")

print("What do you want to do today?\n")

print("\t 1 \t add DNA into a characterized locus\n")

print("\t 2 \t edit an existing gene, e.g., delete or replace\n")

print("\t 3 \t build a custom cassette\n")

Action= input("Your answer: \n")

if Action == "1":

editEmpty()

elif Action == "2":

editExisting()

elif Action == "3":

#we have an excel file where we keep cut site information

#and load it as a pandas dataframe called cutFrame

cutFrame = pd.read_excel("locusTable.xlsx", index_col="cutName")

print("\nThese are the sites we have\t")

print(cutFrame)

print("\nWhich cut site do you want, e.g., ARS208a?\n")

cutName=input("Your answer: ")

# cutName is a string that should correspond to one of the variables

# of the "cutName" column in dataFrame

# cutFrame has the 20nt sequence of the gRNA saved, which we load

cutSequence=cutFrame.loc[cutName,'cutSequence']

# We need to load the chromosome where

location=cutFrame.loc[cutName,'cutChr']+".fasta"

ChromosomeSeq=SeqIO.read(location, "fasta").seq

if ChromosomeSeq.find(cutSequence)==-1:

ChromosomeSeq=ChromosomeSeq.reverse_complement()

if ChromosomeSeq.find(cutSequence)==-1:

print("CAN'T FIND THE CUT SITE IN YOUR SEQUENCE")

StartIndex=ChromosomeSeq.find(cutSequence)

EndIndex=StartIndex+34

UpSeq=ChromosomeSeq[StartIndex-HomologyLength:StartIndex]

DownSeq=ChromosomeSeq[EndIndex:EndIndex+HomologyLength]

UpHomRec = SeqRecord(UpSeq, name=cutName)

DownHomRec = SeqRecord(DownSeq, name=cutName)

print("\nFound your homology regions. What do you want to do to " + cutName + "?\n")

print("\t1\t You have an ORF but want help picking promoter and terminator\n")

print("\t2\t You already have a fabulous cassette and just want to insert it\n\n")

# Coming later

# print("\t3\t You want to construct a donor containing two standard cassettes (pointing away from each other\n")

typeEdit=input("Your answer: ")

if typeEdit=="1":

PromoterRec, orfRecord, TerminatorRec = buildCassette()

fragments=[UpHomRec, PromoterRec, orfRecord, TerminatorRec, DownHomRec]

elif typeEdit == "2":

orfName=input("What's the name of your custom gene or cassette?")

orfSeq=Seq(input("What's the sequence?"))

orfRecord=SeqRecord(orfSeq,name=orfName)

fragments=[UpHomRec, orfRecord, DownHomRec]

elif typeEdit == "3":

print("Your construct will look like this: ")

print("up hom-<terminator1-gene1-promoter1<->promoter2-gene2-terminator2>-downhom")

print("OK, let's build your FIRST cassette")

PromoterRec1, orfRecord1, TerminatorRec1 = buildCassette()

#now in the construction, these will be in the antisense direction, so let's change their sequences

rTerminatorRec1=flipRecord(TerminatorRec1)

rorfRecord1=flipRecord(orfRecord1)

rPromoterRec1=flipRecord(PromoterRec1)

print("OK, let's build your SECOND cassette")

PromoterRec2, orfRecord2, TerminatorRec2 = buildCassette()

fragments=[UpHomRec, rTerminatorRec1, rorfRecord1, rPromoterRec1,PromoterRec2,orfRecord2, TerminatorRec2,DownHomRec]

print(" ")

print("Which locus do you want to edit? Tell me a common name, e.g., \"OAF1\": ")

print("I'm smart and pretty and I can fetch it for you.")

GeneName= input("Your answer: ")

print("OK let me fetch that for you...")

print("")

OrigGeneRecord=fetchGene(GeneName)

#note that this returns a seqrecord

print("")

print("I found "+OrigGeneRecord.features+":")

print(OrigGeneRecord.description)

# We make seqrecords since that's what we carry through later in the program

UpHomRec = fetchNeighbor(OrigGeneRecord, "upstream", HomologyLength )

DownHomRec = fetchNeighbor(OrigGeneRecord, "downstream", HomologyLength )

#print("OK I found them.")

#print(" ")

#print("UpstreamHomology reghhion is")

#print(UpHomRec.seq)

#print(" ")

#print("DownstreamHomology reghhion is")

#print(DownHomRec.seq)

print(" ")

print("What do you want to do to this gene?\n")

print("\t1\t delete the protein coding DNA sequence (CDS)\n")

print("\t2\t replace it with a cassette--I'll help you pick Promoter and Terminator\n")

print("\t3\t replace it with a fabulous one-piece cassette you already designed\n\n")

#print("\t4\t replace the CDS with a custom cassette (soon)")

#print("\t5\t replace a specified region near your target gene (soon)")

print(" ")

Action=input("Your answer: ")

#note that in all the below, we want to have fragments be records

if Action=="1":

fragments=[UpHomRec,DownHomRec]

if Action=="2":

PromoterRec, orfRecord, TerminatorRec = standardCassette()

fragments=[UpHomRec, PromoterRec, orfRecord, TerminatorRec, DownHomRec] #we need to finish buildcassette to add InsertRec here

if Action=="3":

print(" ")

NewGeneName=input("What's the name of the gene you're inserting?")

NewGeneSeq=Seq(input("What's the sequence of your new gene?"))

InsertRec = SeqRecord(NewGeneSeq, name=NewGeneName)

fragments=[UpHomRec, InsertRec, DownHomRec]

if Action=="4":

print("How many pieces (other than homology fragments) are you stitching together.")

Npieces=input("Your answer: ")

output = standardCassette()

fragments=[UpHomRec, DownHomRec] #we need to finish buildcassette to add InsertRec here

N = int(input("How many pieces in your custom cassette: "))

fragments = variableCassette(N)[0]

stitch(fragments)

service = Service("http://yeastmine.yeastgenome.org/yeastmine/service")

template = service.get_template('Gene_GenomicDNA')

rows = template.rows(

E = {"op": "LOOKUP", "value": GeneName, "extra_value": "S. cerevisiae"}

)

# this service seems to return multiple similar genes but we want the first one only, so count

# and it returns information about the gene you want

count=0

for row in rows:

count=count+1

if count==1:

descr= row["description"]

GeneSeq=Seq(row["sequence.residues"])

GeneSysName=row["secondaryIdentifier"]

#let's create a record for the oldGene

GeneRecord = SeqRecord(GeneSeq, id=GeneSysName)

#now let's add some more information to make it useful

GeneRecord.name=GeneName

GeneRecord.features=GeneSysName

GeneRecord.description=descr

# let's load the appropriate chromosome file. The record of the gene we looked up

# contains in the "features" the systematic name, wherein the second letter

# corresponds to chromosome number, e.g., 1=A etc

if NeighborRecord.features[1]=="A":

ChromosomeRec=SeqIO.read("Scer01.fasta", "fasta")

if NeighborRecord.features[1]=="B":

ChromosomeRec=SeqIO.read("Scer02.fasta", "fasta")

if NeighborRecord.features[1]=="C":

ChromosomeRec=SeqIO.read("Scer03.fasta", "fasta")

if NeighborRecord.features[1]=="D":

ChromosomeRec=SeqIO.read("Scer04.fasta", "fasta")

if NeighborRecord.features[1]=="E":

ChromosomeRec=SeqIO.read("Scer05.fasta", "fasta")

if NeighborRecord.features[1]=="F":

ChromosomeRec=SeqIO.read("Scer06.fasta", "fasta")

if NeighborRecord.features[1]=="G":

ChromosomeRec=SeqIO.read("Scer07.fasta", "fasta")

if NeighborRecord.features[1]=="H":

ChromosomeRec=SeqIO.read("Scer08.fasta", "fasta")

if NeighborRecord.features[1]=="I":

ChromosomeRec=SeqIO.read("Scer09.fasta", "fasta")

if NeighborRecord.features[1]=="J":

ChromosomeRec=SeqIO.read("Scer10.fasta", "fasta")

if NeighborRecord.features[1]=="K":

ChromosomeRec=SeqIO.read("Scer11.fasta", "fasta")

if NeighborRecord.features[1]=="L":

ChromosomeRec=SeqIO.read("Scer12.fasta", "fasta")

if NeighborRecord.features[1]=="M":

ChromosomeRec=SeqIO.read("Scer13.fasta", "fasta")

if NeighborRecord.features[1]=="N":

ChromosomeRec=SeqIO.read("Scer14.fasta", "fasta")

if NeighborRecord.features[1]=="O":

ChromosomeRec=SeqIO.read("Scer15.fasta", "fasta")

if NeighborRecord.features[1]=="P":

ChromosomeRec=SeqIO.read("Scer16.fasta", "fasta")

# let's explicitely name the sequences from the seq record

NeighborSeq=NeighborRecord.seq

ChromosomeSeq=ChromosomeRec.seq

# flip the sequence to orient with respect to the old gene

if ChromosomeSeq.find(NeighborSeq)==-1:

ChromosomeSeq=ChromosomeSeq.reverse_complement()

StartIndex=ChromosomeSeq.find(NeighborSeq)

EndIndex=StartIndex+len(NeighborSeq)

if direction=="upstream":

DesiredSeq=ChromosomeSeq[StartIndex-distance:StartIndex]

if direction=="downstream":

DesiredSeq=ChromosomeSeq[EndIndex:EndIndex+distance]

NeighborRec = SeqRecord(DesiredSeq, name=NeighborRecord.name)

return NeighborRec

#print(NeighborRec)

mp = 0

length = 0

primer = Seq("")

seq=currRecord.seq

while mp <= PrimerMaxTm and length <= PrimerMaxLen:

primer = primer + seq[length]

mp = MeltingTemp.Tm_staluc(primer)

length += 1

#let's get the template-binding primer first

primer=getPrimer(currRecord)

#OK let's work on the overhang

maxOhLen=PrimerMaxLen-len(primer)

maxFrac=1

#let's decide on a max overhang length

if round(len(primer)*(OverhangMaxFrac+1)) < 60:

maxOhLen=round(len(primer)*OverhangMaxFrac)

#the index must be an integer!!!

maxOhLen=int(maxOhLen)

ohprimer=prevSeq.seq[-maxOhLen:]+primer #we add the .seq so that it returns a string

#first, the promoter

print("I'm going to build a standard cassette in which promoter is 600nt, terminator 250nt.")

print("")

print("Which PROMOTER do you want to use, e.g., TDH3")

PromoterName=input("Your answer: ")

PromoterGeneRec=fetchGene(PromoterName)

PromoterRec=fetchNeighbor(PromoterGeneRec,"upstream",600)

PromoterRec.name=PromoterRec.name+"ps"

#second, the terminator

print("Which TERMINATOR do you want to use, e.g., ADH1")

TerminatorName = input('Your answer: ')

TerminatorGeneRec=fetchGene(TerminatorName)

TerminatorRec=fetchNeighbor(TerminatorGeneRec,"downstream",250)

TerminatorRec.name=TerminatorRec.name+"ts"

#and last, the gene

print("What do you want to call the CDS you're inserting?")

orfName = input("Your answer: ")

print("What's the sequence")

orfSeq=input("Your answer: ")

orfRecord=SeqRecord(Seq(orfSeq), name=orfName)

insertRec=[PromoterRec,orfRecord,TerminatorRec]

#first, the promoter

print("I'm going to build a standard cassette in which promoter is 600nt, terminator 250nt.")

print("First, which PROMOTER do you want to use, e.g., TDH3")

PromoterName=input("Your answer: ")

PromoterGeneRec=fetchGene(PromoterName)

PromoterRec=fetchNeighbor(PromoterGeneRec,"upstream",600)

PromoterRec.name=PromoterRec.name+"ps"

#second, the terminator

print("Which TERMINATOR do you want to use, e.g., ADH1")

TerminatorName = input('Your answer: ')

TerminatorGeneRec=fetchGene(TerminatorName)

TerminatorRec=fetchNeighbor(TerminatorGeneRec,"downstream",250)

TerminatorRec.name=TerminatorRec.name+"ts"

#and last, the gene

print("What is the name of your gene, e.g., KlGapDH")

orfName = input("Your answer: ")

print("What's the sequence")

orfSeq=input("Your answer: ")

orfRecord=SeqRecord(Seq(orfSeq), name=orfName)

insertRec=[PromoterRec,orfRecord,TerminatorRec]

print("")

print("Let's start building.")

print("")

# Store both name and sequence in a SeqRecord

# Append them to a list

# Return list as fragments to be stitched

records = []

for n in range(N):

name = input("What is the name of sequence " + str(n+1) +":")

sequence = input("What is the sequence of this fragment:")

print("")

Rec = SeqRecord(Seq(sequence), id = str(n+1))

Rec.name = name

records.append(Rec)

variantRecords = []

variantRecords.append(records)

# This only happens if there are variants.

if variants > 0:

print("Time to make those variants you wanted.")

for n in range(variants-1):

name = input("What is the name of variant " + str(n+1) + ":")

sequence = input("What is the sequence of this variant:")

Rec = SeqRecord(Seq(sequence), id = str(n+1))

Rec.name = name

# Make a copy of the original, switch the fragments and add it to the list.

# Deep-copy ensures there are no pointer issues

tempVariant = copy.deepcopy(records)

tempVariant[toVary - 1] = Rec

variantRecords.append(copy.deepcopy(tempVariant))

print("")

# Returns a list of lists of the SeqRecords of the fragments

#this function takes seq records and prints primers

#let's make an empty sequence file

Nfrags=len(fragments)

donor=Seq("")

index=[]

print("")

for i in range (0, Nfrags):

donor=donor+fragments[i]

for i in range (0, Nfrags):

if i==0:

print("Lup"+ fragments[i].name + " " + getPrimer(donor))

print("Rup"+ fragments[i].name + "(" + fragments[i+1].name + ") " + overhangPrimer(fragments[i].reverse_complement(),fragments[i+1].reverse_complement()))

elif i==Nfrags-1:

print("Ldown"+ fragments[i].name + "(" + fragments[i-1].name + ") " + overhangPrimer(fragments[i],fragments[i-1]))

print("Rdown"+ fragments[i].name + " " + getPrimer(donor.reverse_complement()))

else:

print("L"+ fragments[i].name + "(" + fragments[i-1].name + ") " + overhangPrimer(fragments[i],fragments[i-1]))

print("R"+ fragments[i].name + "(" + fragments[i+1].name + ") " + overhangPrimer(fragments[i].reverse_complement(),fragments[i+1].reverse_complement()))

print("")

print("Your donor DNA cassette, has the following bp length and sequence:")

print("")

print(len(donor.seq))

print("")

print(donor.seq)

print("")

from prettytable import from_csv

print("Which of these characterized loci is going to get lucky: ")

fp = open("cutsites.csv", "r")

pt = from_csv(fp)

fp.close()

print(pt)

cutsiteNum = int(input("Choose your cutsite (Leftmost number):"))

print("")

print("You've chosen: ")

print(pt.get_string(start = cutsiteNum-1, end = cutsiteNum))

counter = 0

for row in pt:

counter += 1

if counter == cutsiteNum:

row.border = False

row.header = False

cutsite = row.get_string(fields=["sequence"]).strip()

cutName = row.get_string(fields=["name"]).strip()

chromosome = int(row.get_string(fields=["chromosome"]).strip())

if chromosome >= 10:

filename = "Scer" + str(chromosome) + ".fasta"

else:

filename = "Scer0" + str(chromosome) + ".fasta"

ChromosomeRec=SeqIO.read(filename, "fasta")

ChromosomeSeq = ChromosomeRec.seq

if ChromosomeSeq.find(cutsite) == -1:

ChromosomeSeq = ChromosomeSeq.reverse_complement()

startInd = ChromosomeSeq.find(cutsite)

UpHomology = SeqRecord(ChromosomeSeq[startInd - 1000:startInd])

DownHomology = SeqRecord(ChromosomeSeq[startInd + 30:startInd + 1030])