def insertSeqIntoSeq(seq, insert, homologyF, homologyR):
'''Takes a DNA string as argument and inserts a sequence by homologous recombination'''
seq = seq.lower()
homologyF = homologyF.lower()
homologyR = homologyR.lower()
if seq.find(homologyF) != -1:
beforeHomology = seq.split(homologyF)[0]
else:
print 'Forward homology region does not exist in plasmid'
exit()
homologyR_rc = Primers.reverseComp(homologyR).lower()
if seq.find(homologyR_rc) != -1:
afterHomology = seq.split(homologyR_rc)[1]
else:
print 'Reverse homology region does not exist in plasmid'
exit()
LenSequenceRepacedByInsert = len(seq) - (len(beforeHomology)+len(afterHomology)+len(homologyF) + len(homologyR))
newPlamidSeq = beforeHomology + homologyF + insert + homologyR_rc + afterHomology
before = len(beforeHomology)
return newPlamidSeq, before, LenSequenceRepacedByInsert
genename = linelist[0]
genename2 = genename.split (' ')
genename3 = genename2[0]
promoter = linelist[3]
promoterdict[genename3] = promoter
if PrimerPosition =='Promoter':
for gene1 in genes:
gene = gene1.rstrip('\n')
gene = gene.rstrip('\r')
upstreamseq = str(mydict[gene][1])
try:
promoter_len = int(promoterdict[gene])
promoter_seq = upstreamseq [-promoter_len:]
if direction == 'y':
promoter_seq = Primers.reverseComp(promoter_seq)
# Remember to include if sequence is to be reverse orientation
# promoter_seq = Primers.reverseComp(promoter_seq)
if PrimerType == 'amplification':
primers = Primers.designPrimerpair(promoter_seq, PrimerTM)
primers = homology_F + primers[0], homology_R + primers[1]
if writeAPE == 'y':
AP.SaveToApe(promoter_seq, str(mydict[gene][0])+' '+gene)
if plas == 'y':
newPlasmid = AP.replaceAPEseq(MyPlasmid, promoter_seq, homology_F , homology_R ,str(mydict[gene][0]) )
newPlasmid = AP.insertFeature(newPlasmid, promoter_seq, label = str(mydict[gene][0]), colour = 'cyan')
AP.SaveToApe(newPlasmid, str(mydict[gene][0]))
elif PrimerType =='homology':
primers = Primers.designHomologyPair(promoter_seq)
primers = primers[0] + amplify_F, primers[1] + amplify_R
