def main():
cmd_prefix = args.get(0) if args.get(0) else ""
swga_cmd = colored.green(os.path.join(cmd_prefix,"swga"))
puts(colored.blue('#'*70))
with indent(2, quote=colored.blue("#")):
puts(message.format(swga_cmd = swga_cmd,
prefix = colored.magenta(cmd_prefix)))
puts(colored.blue('#'*70))
def pprint_args(self):
if not self.args:
return
else:
swga.message(colored.green("Command: " + self.name))
with indent(2, quote='-'):
for arg, val in self.args.iteritems():
if val is None or val == "":
val = colored.red("None")
swga.message(colored.blue("{}: {}".format(arg, val)))
def summary(primer_db, fg_length, bg_length):
db = swga.database.init_db(primer_db)
db.connect()
swga.database.create_tables(drop=False)
avg_fg_bind, avg_bg_bind, nprimers = (
Primer
.select(fn.Avg(Primer.fg_freq),
fn.Avg(Primer.bg_freq),
fn.Count(Primer.seq))
.scalar(as_tuple=True))
if (avg_fg_bind is None) or (avg_bg_bind is None):
raise swga.error(
"Could not calculate summary statistics; database may be corrupt")
fg_bind_ratio = avg_fg_bind / float(fg_length)
bg_bind_ratio = avg_bg_bind / float(bg_length)
nactive = Primer.select().where(Primer.active==True).count()
min_tm, max_tm, avg_tm = (
Primer
.select(fn.Min(Primer.tm),
fn.Max(Primer.tm),
fn.Avg(Primer.tm))
.where(Primer.active==True)
.scalar(as_tuple=True))
nsets = Set.select(fn.Count(Set._id)).scalar()
if nsets > 0:
bs = Set.select().order_by(Set.score).limit(1).get()
bs_primers = ", ".join(swga.database.get_primers_for_set(bs._id)).strip()
best_set = bs._id
bs_size = bs.set_size
bs_score = bs.score
bs_stats = "- "+"\n - ".join(
fmtkv(k, v)
for k, v in bs.__dict__['_data'].items()
if k not in ["_id", "pids", "score"]
)
version_header = (
"---------------------\n"
"==== SWGA v{version} ====\n"
"---------------------\n"
.format(version=swga.__version__)
)
summary_msg = """
{version_header}
PRIMER SUMMARY
---------------
There are {nprimers} primers in the database.
{nactive} are marked as active (i.e., they passed filter steps and will be used to find sets of compatible primers.) {ifzero_primers_msg}
The average number of foreground genome binding sites is {avg_fg_bind:.0f}.
(avg binding / genome_length = {fg_bind_ratio:05f})
The average number of background genome binding sites is {avg_bg_bind:.0f}.
(avg binding / genome_length = {bg_bind_ratio:05f})
{melting_tmp_msg}
SETS SUMMARY
---------------
There are {nsets} sets in the database.
{set_msg}---------------
Report generated from {primer_db}
"""
ifzero_primers_msg = colored.green(
"Run `swga filter` to identify primers to use."
if nactive == 0 else "")
melting_tmp_msg = (
"""The melting temp of the primers ranges between {min_tm:.2f}C and {max_tm:.2f}C with an average of {avg_tm:.2f}C."""
if nactive > 0 and min_tm and max_tm else
"No melting temps have been calculated yet.")
ifzero_sets_msg = colored.green(
"Run `swga find_sets` after identifying valid primers to begin collecting sets.\n")
set_msg = ("""
The best scoring set is #{best_set}, with {bs_size} primers and a score of {bs_score:03f}.\nVarious statistics:
{bs_stats}
The primers in Set {best_set} are:
{bs_primers}
""" if nsets > 0 else ifzero_sets_msg)
primer_db = os.path.abspath(primer_db)
nprimers = colored.blue(nprimers, bold=True)
nactive = colored.blue(nactive, bold=True)
nsets = colored.blue(nsets, bold=True)
set_msg = set_msg.format(**locals())
melting_tmp_msg = melting_tmp_msg.format(**locals())
version_header = colored.green(version_header)
summary_msg = summary_msg.format(**locals())
with indent(2):
puts(max_width(summary_msg, 80))