def IntermLineCompile(template_filename, primer_sense, primer_antisense,
interest_regions):
"""
Merges input of primer sequences with the gene template; returns FP, RP, Template that is to be fed into the VirtualPCR;
"""
template = open(template_filename)
Outflank = re.findall('\d+', template_filename.split('_')[1])[0]
outflank = int(Outflank)
template.readline()
#read entire FASTA sequence as one string (includes hang
gene_seq_h = [seqs.replace('\n', '') for seqs in template.readlines()]
gene_seq_h = ''.join(gene_seq_h)
template.close()
#gene_seq excludes the hang:
if outflank != 0:
gene_seq = gene_seq_h[outflank:-outflank]
#gene_seg_f is formatted, combining the hangs as small caps
gene_seq_f = gene_seq_h[:outflank].lower(
) + gene_seq + gene_seq_h[-outflank:].lower()
else:
gene_seq = gene_seq_h
gene_seq_f = gene_seq
#translate codon sequence to AA sequence w numbers
aa_seq = VirtualPCR.SeqToAA(gene_seq)
#visualize the target relativet o entire aa sequence; basically, scan the aa sequence, draw it as a ---, replace teh dash w the aa target name if it matches.
if interest_regions != ['']:
aa_viz = ['*'] * aa_seq.count('_')
for region in interest_regions:
for aa in aa_seq.split('_'):
#if there is a perfect match, return them in uppercase
if aa == region.strip():
aa_viz[aa_seq.split('_').index(aa)] = aa.upper()
#if just numbers match, return in lowercase
elif re.findall('\d+',
aa) == re.findall('\d+', region.strip()):
aa_viz[aa_seq.split('_').index(aa)] = aa
else:
next
aa_viz = ''.join(aa_viz)
#if no target region is specified, translate entire aa sequence
else:
aa_viz = aa_seq
#if outflanked, add '-' to the ends
aa_viz = outflank / 3 * '-' + aa_viz + outflank / 3 * '-'
#find the positions of the sense and anti-sense primers relative to template; if not found, return (No exact match)
sense_postest = re.search(primer_sense, gene_seq, flags=0)
if sense_postest == None:
sense_pos = "Not in range"
else:
sense_pos = sense_postest.span()
#Note: use the reverse comp for the antisense check
antisense_postest = re.search(VirtualPCR.CompRev(primer_antisense),
gene_seq,
flags=0)
if antisense_postest == None:
antisense_pos = "Not in range"
else:
antisense_pos = antisense_postest.span()
#open the input file, read in the primer sequences
InputLineData = [
gene_seq_f, aa_viz, primer_sense, primer_antisense, sense_pos,
antisense_pos
]
InputLineDataStr = MakeString(InputLineData)
return (InputLineDataStr)
