def main():
options, args = interface()
conf = ConfigParser.ConfigParser()
conf.read(options.input)
# create a temporary table in memory for the results
if options.keepdb:
dir, name = os.path.split(options.output)
name = name.split('.')[0] + '.sqlite'
db_path = os.path.join(dir, name)
conn = sqlite3.connect(db_path)
else:
conn = sqlite3.connect(':memory:')
cur = conn.cursor()
create_database(cur)
settings = get_primer3_settings()
# make sure we send it the correct version of primer3
p3 = primer.Primers(binary='primer3_long')
# trick the module to think we've actually designed primers
p3.primers_designed = True
p3.primers = {0:
{'PRIMER_LEFT_SEQUENCE':options.left, 'PRIMER_RIGHT_SEQUENCE':options.right},
'metadata':None
}
# check normal primers
p3.check(settings)
for k in p3.checked_primers:
if p3.checked_primers[k]:
p3.checked_primers[k]['SECTION'] = 'None'
p3.checked_primers[k]['CYCLES'] = 0
p3.checked_primers[k]['TAG'] = None
p3.checked_primers[k]['UNMODIFIED'] = 1
p3.checked_primers[k]['PAIR_HAIRPIN_EITHER'] = 0
# add some information that will be missing from these
p3.checked_primers[k]['PRIMER_LEFT_TAG'] = None
p3.checked_primers[k]['PRIMER_RIGHT_TAG'] = None
p3.checked_primers[k]['PRIMER_LEFT_TAG_COMMON_BASES'] = None
p3.checked_primers[k]['PRIMER_RIGHT_TAG_COMMON_BASES'] = None
for p in ['PRIMER_LEFT_PROBLEMS', 'PRIMER_RIGHT_PROBLEMS']:
if p not in p3.checked_primers[k].keys():
p3.checked_primers[k][p] = None
elif 'Hairpin stability too high;' in p3.checked_primers[k][p]:
p3.checked_primers[k]['PAIR_HAIRPIN_EITHER'] = 1
#pdb.set_trace()
insert_primers(cur, p3.checked_primers[k])
#f = open(options.input, 'rU')
# [[name, tag]]
#tags = [line.strip().split(',') for line in f]
if not options.section:
for section in conf.sections():
tags = get_tag_array(conf.items(section))
design_and_store_primers(options, cur, section, tags, p3, settings)
elif options.section:
tags = get_tag_array(conf.items(options.section))
design_and_store_primers(options, cur, options.section, tags, p3, settings)
conn.commit()
# close the tag input file - it's not needed anymore
#f.close()
if options.output:
write_results(cur, options.output, options.sort_keys)
def main():
options, args = interface()
conf = ConfigParser.ConfigParser()
conf.read(options.input)
adapters = {}
if not options.section:
for section in conf.sections():
tags = get_tag_array(conf.items(section))
adapters = add_tags_to_adapters(adapters, section, options.fprime, options.tprime, tags, options.revcomp)
elif options.section:
tags = get_tag_array(conf.items(options.section))
adapters = add_tags_to_adapters(adapters, options.section, options.fprime, options.tprime, tags, options.revcomp)
show_results(adapters, options.suppress)
def main():
options, args = interface()
conf = ConfigParser.ConfigParser()
conf.read(options.input)
adapters = {}
if not options.section:
for section in conf.sections():
tags = get_tag_array(conf.items(section))
adapters = add_tags_to_adapters(adapters, section, options.fprime,
options.tprime, tags,
options.revcomp)
elif options.section:
tags = get_tag_array(conf.items(options.section))
adapters = add_tags_to_adapters(adapters, options.section,
options.fprime, options.tprime, tags,
options.revcomp)
show_results(adapters, options.suppress)
def main():
"""main loop"""
options, arg = interface()
conf = ConfigParser.ConfigParser()
conf.read(options.input)
if options.hamming:
vector_distance = numpy.vectorize(hammng)
else:
vector_distance = numpy.vectorize(levenshtein)
bad = {}
if not options.section:
for section in conf.sections():
tags = get_tag_array(conf.items(section))
names = get_name_array(conf.items(section))
bad = get_section_results(options, bad, tags, section, vector_distance)
elif options.section:
tags = get_tag_array(conf.items(options.section))
names = get_name_array(conf.items(options.section))
bad = get_section_results(options, bad, tags, options.section, vector_distance)
if options.minimums:
print_minimums(conf, names, tags, bad, options.verbose)
elif options.distances:
print_distances(conf, options, names, tags, bad, options.verbose)
def main():
"""main loop"""
options, arg = interface()
conf = ConfigParser.ConfigParser()
conf.read(options.input)
if options.hamming:
vector_distance = numpy.vectorize(hammng)
else:
vector_distance = numpy.vectorize(levenshtein)
bad = {}
if not options.section:
for section in conf.sections():
tags = get_tag_array(conf.items(section))
names = get_name_array(conf.items(section))
bad = get_section_results(options, bad, tags, section, vector_distance)
elif options.section:
tags = get_tag_array(conf.items(options.section))
names = get_name_array(conf.items(options.section))
bad = get_section_results(options, bad, tags, options.section, vector_distance)
if options.minimums:
print_minimums(conf, names, tags, bad, options.verbose)
elif options.distances:
print_distances(conf, options, names, tags, bad, options.verbose)
def main():
options, args = interface()
conf = ConfigParser.ConfigParser()
conf.read(options.input)
# create a temporary table in memory for the results
if options.keepdb:
dir, name = os.path.split(options.output)
name = name.split('.')[0] + '.sqlite'
db_path = os.path.join(dir, name)
conn = sqlite3.connect(db_path)
else:
conn = sqlite3.connect(':memory:')
cur = conn.cursor()
create_database(cur)
settings = get_primer3_settings()
# make sure we send it the correct version of primer3
p3 = primer.Primers(binary='primer3_long')
# trick the module to think we've actually designed primers
p3.primers_designed = True
p3.primers = {
0: {
'PRIMER_LEFT_SEQUENCE': options.left,
'PRIMER_RIGHT_SEQUENCE': options.right
},
'metadata': None
}
# check normal primers
p3.check(settings)
for k in p3.checked_primers:
if p3.checked_primers[k]:
p3.checked_primers[k]['SECTION'] = 'None'
p3.checked_primers[k]['CYCLES'] = 0
p3.checked_primers[k]['TAG'] = None
p3.checked_primers[k]['UNMODIFIED'] = 1
p3.checked_primers[k]['PAIR_HAIRPIN_EITHER'] = 0
# add some information that will be missing from these
p3.checked_primers[k]['PRIMER_LEFT_TAG'] = None
p3.checked_primers[k]['PRIMER_RIGHT_TAG'] = None
p3.checked_primers[k]['PRIMER_LEFT_TAG_COMMON_BASES'] = None
p3.checked_primers[k]['PRIMER_RIGHT_TAG_COMMON_BASES'] = None
for p in ['PRIMER_LEFT_PROBLEMS', 'PRIMER_RIGHT_PROBLEMS']:
if p not in p3.checked_primers[k].keys():
p3.checked_primers[k][p] = None
elif 'Hairpin stability too high;' in p3.checked_primers[k][p]:
p3.checked_primers[k]['PAIR_HAIRPIN_EITHER'] = 1
#pdb.set_trace()
insert_primers(cur, p3.checked_primers[k])
#f = open(options.input, 'rU')
# [[name, tag]]
#tags = [line.strip().split(',') for line in f]
if not options.section:
for section in conf.sections():
tags = get_tag_array(conf.items(section))
design_and_store_primers(options, cur, section, tags, p3, settings)
elif options.section:
tags = get_tag_array(conf.items(options.section))
design_and_store_primers(options, cur, options.section, tags, p3,
settings)
conn.commit()
# close the tag input file - it's not needed anymore
#f.close()
if options.output:
write_results(cur, options.output, options.sort_keys)
