from pydna.readers import read
from pydna.parsers import parse
from pydna.parsers import parse_primers
from pydna.design import primer_design
from pydna.amplify import pcr
from pydna.amplify import Anneal

pYPKa = read("pYPKa.gb")

from Bio.Restriction import ZraI, EcoRV

pYPKa_ZraI  = pYPKa.linearize(ZraI)
pYPKa_EcoRV = pYPKa.linearize(EcoRV)

ins = read("FBA1.gb")

fp_tail = "ttaaat"
rp_tail = "taattaa"

ins = primer_design(ins)
fp = fp_tail + ins.forward_primer
rp = rp_tail + ins.reverse_primer

print(fp.format("fasta"))
print(rp.format("fasta"))
with open("new_primers.txt", "a+") as f:
    f.write(fp.format("fasta"))
    f.write(rp.format("fasta"))

prd = pcr(fp, rp, ins)

len(prd)

prd.figure()

prd.program()

pYPKa_Z_FBA1 = (pYPKa_ZraI  + prd).looped().synced(pYPKa)
pYPKa_E_FBA1 = (pYPKa_EcoRV + prd).looped().synced(pYPKa)

pYPKa_Z_FBA1b = (pYPKa_ZraI  + prd.rc()).looped().synced(pYPKa)
pYPKa_E_FBA1b = (pYPKa_EcoRV + prd.rc()).looped().synced(pYPKa)

p = { x.id: x for x in parse_primers("standard_primers.txt") }

Anneal( (p['577'], p['342'], fp), pYPKa_Z_FBA1).products

Anneal( (p['577'], p['342'], fp), pYPKa_Z_FBA1b).products

Anneal( (p['577'], p['342'], fp), pYPKa).products

Anneal( (p['577'], p['342'], fp), pYPKa_E_FBA1).products

Anneal( (p['577'], p['342'], fp), pYPKa_E_FBA1b).products


print(pYPKa_Z_FBA1.cseguid())
print(pYPKa_E_FBA1.cseguid())

pYPKa_Z_FBA1.locus = "pYPKa_Z_FBA1"[:16]
pYPKa_E_FBA1.locus = "pYPKa_Z_FBA1"[:16]

pYPKa_Z_FBA1.stamp()
pYPKa_E_FBA1.stamp()

pYPKa_Z_FBA1.write("pYPKa_Z_FBA1.gb")
pYPKa_E_FBA1.write("pYPKa_E_FBA1.gb")

import pydna
reloaded = read("pYPKa_Z_FBA1.gb")
reloaded.verify_stamp()

import pydna
reloaded = read("pYPKa_E_FBA1.gb")
reloaded.verify_stamp()