from pydna import open_config_folder

# NBVAL_SKIP
open_config_folder()

"""
Explanation: Primer screening with pydna
This notebook shown how to screen a list of primers against a DNA sequence to find primers that bind the sequence. 
In this example, the built in primer list and ApE is used. The correct path for both ApE and the primer list has to be added to the pydna.ini file. See an example below.

To open the config folder, call this function:
End of explanation
"""


from pydna.readers import read

dna = read("pYPKa.gb")

# NBVAL_SKIP
from pydna.myprimers import list_primers
from pydna.amplify import Anneal

# NBVAL_SKIP
ann = Anneal(list_primers, dna)

# NBVAL_SKIP
from pydna.editor import ape

# NBVAL_SKIP
ape(ann.template)

"""
Explanation: if necessary, add a line like:
ape=tclsh /home/bjorn/.ApE/apeextractor/ApE.vfs/lib/app-AppMain/AppMain.tcl

and:
primers=/home/bjorn/Dropbox/wikidata/Primers.txt

The text file containing primer has to contain sequences in fasta or Genbank format.
End of explanation
"""


