def bsai(files, verbose = verbose):
'''Check for bsaI compatibility, uniqueness etc and finally print a list of
primers with six nucleotides appended'''
#CHECK EACH PRIMER FILE SEPERATELY
for f in files:
sw('\nFILE {0}:\n\n'.format(f))
primers = readfiles([f])
#CHECK BSAI SITES IN ONE FILE AT A TIME
sw('checking for bsai sites:\n')
overhangs = bsai_overhangs(primers)
olist =[ o[1] for o in overhangs]
overhangs_rc = [str(zutils.reverse_complement(oh) ).upper()
for oh in olist]
print 'len overhang set: {0} '.format(len(set(olist)))
print 'len overhang union rc: {0} '.format(len(set(olist+overhangs_rc)))
assert( len(set(olist)) * 2 == len(set(olist+overhangs_rc)))
print 'Checking for palindromes... '
print sorted(olist+overhangs_rc)
print 'none exist!'
pseqs = primer_seqs(primers)
ntot = len(primers); np = len(pseqs)
#DO ANY PRIMERS LACK A BSAI SITE?
fails = [(k,v)
for k,v in pseqs.iteritems()
if v.upper()[:6] != 'GGTCTC']
if len(fails) == 0: sw('SUCCESS\n')
else:sw('FAILURE'+'{0}\n'.format(fails)); return(1)
#CHECK LINKER PAIRING
sw('\nchecking overhangs:\n')
#EVERY LINKER IS PAIRED ONCE (VECTOR BACKBONE IS PRIMED)
if verbose: sw('\n'.join([o[1] for o in overhangs])+'\n')
if len(set([o[1] for o in overhangs])) == np / 2.:
sw('SUCCESS\nevery primer appears paired:\n')
sw('{0}\n'.format('\n'.join([' <--> '.join(['{0:5}'.format(elt[0]) for elt in list(g)] )
for k , g in it.groupby(
sorted(overhangs, key = lambda x:x[1]),
key = lambda x: x[1])])))
#TWO LINKERS ARE UNPAIRED (NO VECTOR PRIMERS)
elif len(set([o[1] for o in overhangs])) ==np / 2. + 1:
sw('SUCCESS\nevery primer appears paired:\n')
sw('{0}\n'.format('\n'.join(\
sort_good([
' <--> '.join(\
sort_good(['{0:5}'.format(elt[0])
for elt in list(g)]
))
for k , g in it.groupby( sorted(overhangs, key = lambda x:x[1]),
key = lambda x: x[1])]))))
#SOMETHING WEIRD IS GOING ON
else:
sw('FAILURE\n')
grps =dict([(k,list(g)) for k , g in it.groupby(
sorted(overhangs, key = lambda x:x[1]),
key = lambda x: x[1])])
sw('{0}\n'.format(
'\n'.join( '{0} share {1}'.format(
(', '.join([e[0] for e in elt[1]])),
elt[0])
for elt in grps.iteritems()
if len(elt[1]) > 2)))
#IF THIS IS BEING RUN INTERACTIVELY, CRY FOUL!
if __name__ != '__main__': raise Exception()
return(1)
sw('\nEverything appears to be OK\n')
#NOW READ ALL OF THE FILES AT ONCE AND PRINT
primers = readfiles(files)
sw('printing primers:\n')
sw('\n'.join(sorted(['{0}; {1}; '.format(*p) for p in bsai_print_final(primers)])))
def bsai_overhangs(primers):
'''Given a dict of pcr products with primers, grab the 4 nt BsaI overhangs'''
return list(it.chain(*[((p['fname'],p['fwd'][7:11].upper()),
(p['rname'],''.join(zutils.reverse_complement(\
p['rev'][7:11].upper()))))
for p in primers.values()]))