def run(self):
primers = Primers(self.input)
try:
(primers.update_melt_temps().update_locations(
self.fg_genome_fp).activate())
except AttributeError as e:
warn("Error updating database: '{}'".format(e.message))
raise e
def run(self):
primers = Primers(self.input)
try:
(primers
.update_melt_temps()
.update_locations(self.fg_genome_fp)
.activate())
except AttributeError as e:
warn("Error updating database: '{}'".format(e.message))
raise e
def parse_args(self, argv, quiet=False):
args, unknown = self.parser.parse_known_args(argv)
self.args = vars(args)
self.unknown = unknown
for k, v in self.args.items():
setattr(self, k, v)
if not quiet:
self._pprint_args()
if len(self.args) > 0 and all(v is None for k, v in self.args.items()):
warn(
u'[swga {0:s}]: All parameters are missing- this may indicate a corrupt or missing parameters file.'
.format(self.name))
def parse_args(self, argv, quiet=False):
args, unknown = self.parser.parse_known_args(argv)
self.unknown = unknown
self.args = vars(args)
self.kwargs_as_args(**self.args)
if not quiet:
self.pprint_args()
if len(self.args) > 0 and all(v is None for k, v in self.args.items()):
swga.warn(
"[swga %s]: All parameters are missing- ",
"this may indicate a corrupt or missing parameters file."
% self.name)
def process_lines(self, setfinder_lines):
passed = processed = 0
smallest_max_dist = float('inf')
try:
for line in setfinder_lines:
try:
primer_ids, bg_dist_mean = score.read_set_finder_line(line)
except ValueError:
warn("Could not parse line:\n\t" + line)
continue
primers = Primers.select_by_ids(primer_ids)
processed += 1
set_score, variables, max_dist = score.score_set(
primers=primers,
max_fg_bind_dist=self.max_fg_bind_dist,
bg_dist_mean=bg_dist_mean,
chr_ends=self.chr_ends,
score_fun=self.score_fun,
interactive=False
)
if max_dist < smallest_max_dist:
smallest_max_dist = max_dist
message(
STATUS_LINE.format(processed, passed, smallest_max_dist),
newline=False)
# Return early if the set doesn't pass
if set_score is False:
continue
else:
passed += 1
Set.add(
_id=passed,
primers=primers,
score=set_score,
scoring_fn=self.score_expression,
**variables)
if passed >= self.max_sets:
message("\nDone (scored %i sets)" % passed)
break
finally:
# Raises a GeneratorExit inside the find_sets command, prompting it
# to quit the subprocess
setfinder_lines.close()
def process_lines(self, setfinder_lines):
passed = processed = 0
smallest_max_dist = float('inf')
try:
for line in setfinder_lines:
try:
primer_ids, bg_dist_mean = score.read_set_finder_line(line)
except ValueError:
warn("Could not parse line:\n\t" + line)
continue
primers = Primers.select_by_ids(primer_ids)
processed += 1
set_score, variables, max_dist = score.score_set(
primers=primers,
max_fg_bind_dist=self.max_fg_bind_dist,
bg_dist_mean=bg_dist_mean,
chr_ends=self.chr_ends,
score_fun=self.score_fun,
interactive=False)
if max_dist < smallest_max_dist:
smallest_max_dist = max_dist
message(STATUS_LINE.format(processed, passed,
smallest_max_dist),
newline=False)
# Return early if the set doesn't pass
if set_score is False:
continue
else:
passed += 1
Set.add(_id=passed,
primers=primers,
score=set_score,
scoring_fn=self.score_expression,
**variables)
if passed >= self.max_sets:
message("\nDone (scored %i sets)" % passed)
break
finally:
# Raises a GeneratorExit inside the find_sets command, prompting it
# to quit the subprocess
setfinder_lines.close()
def calculate_bg_dist_mean(primers, bg_length):
"""Calculate the mean distance between binding sites on the bg genome.
:param bg_length: the total length of the background genome.
"""
total_bg_freq = sum(p.bg_freq for p in primers)
if total_bg_freq == 0:
warn(
"No primers appear in the background genome: "
"bg_dist_mean set as infinite")
bg_dist_mean = float('Inf')
else:
bg_dist_mean = float(
bg_length) / sum(p.bg_freq for p in primers)
return bg_dist_mean
def read_primer_list(lines):
"""Read in a list of primers and return their records from the db.
:param lines: a list of primer sequences, one per line; anything after the
first whitespace is ignored.
"""
seqs = [re.split(r'[ \t]+', line.strip('\n'))[0] for line in lines]
primers = list(Primer.select().where(Primer.seq << seqs).execute())
if len(primers) < len(seqs):
primer_seqs = [p.seq for p in primers]
missing = [_ for _ in seqs if _ not in primer_seqs]
for seq in missing:
warn(
seq + ' not in the database; skipping. Add it manually with '
'`swga count --input <file>` ')
return primers
def init_db(db_fname, create_if_missing=False):
'''
Initializes the database at the file path specified.
If `create_if_missing` is True, it will create the database if it can't be
found. Otherwise, it exits with an error (SystemExit).
'''
if db_fname is None:
swga.error("Primer db name cannot be `None`: corrupt preferences.cfg?")
elif db_fname == ":memory:":
swga.warn("Creating in-memory primer database; this may not work.")
elif not os.path.isfile(db_fname) and not create_if_missing:
# Exits here
swga.error(
"Primer db not found at '%s': specify different filename or "
"re-run `swga count`" % db_fname, exception=False
)
db.init(db_fname)
return db
def _hits_per_record(self):
'''
Calculates the number of bases covered by primers in each record, and
yields the record name, midpoint of the record, and number of hits as
a tuple.
'''
record_ends = swga.locate.chromosome_ends(self.fg_genome_fp)
for record_name, ends in record_ends.iteritems():
record_length = ends[1] + 1
# Check window size <= record_length and fix if not
this_window_size = self.window_size
if this_window_size > record_length:
this_window_size = record_length
swga.warn(
"In [{}]: window size larger than record; set to {}"
.format(record_name, this_window_size))
# Check step size is compatible with window size and fix if not
this_step_size = self.step_size
if this_step_size > this_window_size:
this_step_size = this_window_size
swga.warn(
"In [{}]: step size larger than window size ({}), set to {}"
.format(record_name, this_window_size, this_step_size))
# Count the number of primers that bind to any given nucleotide
# in the current record
counter = Counter()
for primer in self.set.primers:
k = len(primer.seq)
locations = primer.locations()
for l in locations[record_name]:
counter.update(Counter(xrange(l, l + k)))
starting_positions = xrange(
0, int(record_length - this_window_size), this_step_size)
for start in starting_positions:
end = start + this_window_size
midpoint = (end + start) / 2
# Add each base's count to get the number of bases covered
hits = sum([counter[i] for i in xrange(start, end)])
yield record_name, midpoint, hits
def check_create_tables(primer_db):
if os.path.isfile(primer_db):
swga.warn("Existing database found at %s" % os.path.abspath(primer_db))
swga.warn("This will reset the entire database!")
click.confirm("Are you sure you want to proceed?", abort=True)
database.create_tables()