# load SeqUtil methods
sys.path.append('code')
import SeqUtil
importlib.reload(SeqUtil)
lenTargetPeptide = len(target)
lenTargetDna = lenTargetPeptide*3
foundDnas = [] # storage of target dan sequences
## search amino acids in forward direction
for start in range(0,3): # loop for reading frame start
curDna = dna[start:]
curRna = SeqUtil.dna2rna(curDna)
peptides = SeqUtil.rna2peptide(curRna, mapFile='./data/RNA_codon_table_1.txt')
pepStartIndex = 0
for pep in peptides:
# find positions of target in peptide
targetPositions = [pos for pos in range(0, len(pep)) if pep[pos:(pos+lenTargetPeptide)]==target]
# get corresponding dna sequence and save
targetDnas = [curDna[(pepStartIndex+pos*3):(pepStartIndex+pos*3+lenTargetDna)] for pos in targetPositions]
foundDnas.extend(targetDnas)
# update pepStartIndex for the next peptide
pepStartIndex = pepStartIndex + (len(pep)+1)*3
