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bugged stringlengths 4 228k	fixed stringlengths 0 96.3M	__index_level_0__ int64 0 481k
def set_source(self, source): """ Define an alternative source for the colormap. source can be any other matplotlib colormap object or its registered name, a NumPy array with one RGB triplet per row or the name of a textfile with one RGB triplet per line. Values should be between 0.0 and 1.0. """ self.source = source...	def set_source(self, source): """ Define an alternative source for the colormap. source can be any other matplotlib colormap object or its registered name, a NumPy array with one RGB triplet per row or the name of a textfile with one RGB triplet per line. Values should be between 0.0 and 1.0. """ self.source = source...	480,500
def uniconvw_run(): file=None icon=None _pkgdir = __path__[0] app_ver = string.strip(open(os.path.join(_pkgdir, 'VERSION')).read())	defuniconvw_run():file=Noneicon=None_pkgdir=__path__[0]app_ver=string.strip(open(os.path.join(_pkgdir,'VERSION')).read())	480,501
def uniconvw_run(): file=None icon=None _pkgdir = __path__[0] app_ver = string.strip(open(os.path.join(_pkgdir, 'VERSION')).read())	def uniconvw_run(): file=None icon=None _pkgdir = __path__[0] app_ver = string.strip(open(os.path.join(_pkgdir, 'VERSION')).read())	480,502
def clean_code(self, text): # remove XML comments text = re.sub(self.RE_XMLCOMMENT, '', text) # remove preprocessor directions text = re.sub(self.RE_PREPROCESSOR, '', text) # substitute multilines with one line text = re.sub(self.RE_MULTILINES, "", text) return text	def clean_code(self, text): # remove XML comments text = re.sub(self.RE_XMLCOMMENT, '', text) # remove preprocessor directions text = re.sub(self.RE_PREPROCESSOR, '', text) # substitute multilines with one line text = re.sub(self.RE_MULTILINES, "", text) return text	480,503
def write_function(self, fn, f): f.writelines([ r'\begin{functiondef}{', self.cmd('returnvalue', fn.return_value), ' ', self.cmd('function', fn.name), '(', ]) if fn.parameters: params = ", ".join(map(lambda s: self.cmd('textbf', s), fn.parameters)) f.writelines([params]) f.writelines([')}\n\n'])	def write_function(self, fn, f): f.writelines([ r'\begin{functiondef}{', self.cmd('returnvalue', fn.return_value), ' ', self.cmd('function', fn.name), '(', ]) if fn.parameters: params = ", ".join(map(lambda s: self.cmd('textbf', s), fn.parameters)) f.writelines([params]) f.writelines([')}\n\n'])	480,504
def write_function(self, fn, f): f.writelines([ r'\begin{functiondef}{', self.cmd('returnvalue', fn.return_value), ' ', self.cmd('function', fn.name), '(', ]) if fn.parameters: params = ", ".join(map(lambda s: self.cmd('textbf', s), fn.parameters)) f.writelines([params]) f.writelines([')}\n\n'])	def write_function(self, fn, f): f.writelines([ r'\begin{functiondef}{', self.cmd('returnvalue', fn.return_value), ' ', self.cmd('function', fn.name), '(', ]) if fn.parameters: params = ", ".join(map(lambda s: self.cmd('textbf', s), fn.parameters)) f.writelines([params]) f.writelines([')}\n\n'])	480,505
def write_function(self, fn, f): lines = [ '<div class="function_definition">\n', '<a name="function_%s">' % fn.name, '<h3><span class="type">%s</span> <span class="keyword">function</span> <span class="subroutine">%s</span>(<div class="parameters">' % (fn.return_value, fn.name) ] f.writelines(lines) subs = [] for var ...	def write_function(self, fn, f): lines = [ '<div class="function_definition">\n', '<a name="function_%s">' % fn.name, '<h3><span class="type">%s</span> <span class="keyword">function</span> <span class="subroutine">%s</span>(<div class="parameters">' % (fn.return_value, fn.name) ] f.writelines(lines) subs = [] for var ...	480,506
def interpret(self, nodes): "Extract information from the nodes."	def interpret(self, nodes): "Extract information from the nodes."	480,507
def extract_subroutine(self, node, text): "Extract subroutine from source code."	defextract_subroutine(self,node,text):"Extractsubroutinefromsourcecode."	480,508
def extract_subroutine(self, node, text): "Extract subroutine from source code."	def extract_subroutine(self, node, text): "Extract subroutine from source code."	480,509
def extract_variables(self, text, l): "Extract variable and group information from source code."	def extract_variables(self, text, l): "Extract variable and group information from source code."	480,510
def end_group(scanner, token): if not self.active_group.variables: error(15, 'No variable found in group: %s' % self.active_group.description) self.active_group = None self.current_comment = None	def end_group(scanner, token): if not self.active_group.variables: error(15, 'No variable found in group: %s' % self.active_group.description) self.active_group = None self.current_comment = None	480,511
def commentblock(scanner, token): self.current_comment = token.strip()	def commentblock(scanner, token): self.current_comment = token.strip()	480,512
def blank_lines(scanner, token): self.current_comment = None	def blank_lines(scanner, token): self.current_comment = None	480,513
def variable_definition(scanner, token): match = re.search(self.VARIABLE, token) if match: m = match.groups() vartype = m[1].split(",")[0].strip() if self.current_comment: self.current_comment = self.clean_description(self.current_comment) v = Variable(m[2], vartype, self.current_comment) else: v = Variable(m[2], varty...	def variable_definition(scanner, token): match = re.search(self.VARIABLE, token) if match: m = match.groups() vartype = m[1].split(",")[0].strip() if self.current_comment: self.current_comment = self.clean_description(self.current_comment) v = Variable(m[2], vartype, self.current_comment) else: v = Variable(m[2], varty...	480,514
def variable_definition(scanner, token): match = re.search(self.VARIABLE, token) if match: m = match.groups() vartype = m[1].split(",")[0].strip() if self.current_comment: self.current_comment = self.clean_description(self.current_comment) v = Variable(m[2], vartype, self.current_comment) else: v = Variable(m[2], varty...	def variable_definition(scanner, token): match = re.search(self.VARIABLE, token) if match: m = match.groups() vartype = m[1].split(",")[0].strip() if self.current_comment: self.current_comment = self.clean_description(self.current_comment) v = Variable(m[2], vartype, self.current_comment) else: v = Variable(m[2], varty...	480,515
def write_interface(self, interface, description, f): f.writelines([self.cmd('interface', interface), '\n']) f.writelines([self.env('desc', description), '\n'])	def write_interface(self, interface, description, f): f.writelines([self.cmd('interface', interface), '\n']) f.writelines([self.env('desc', description), '\n'])	480,516
def write_subroutine(self, sub, f): f.writelines([ r'\begin{subroutinedef}{', self.cmd('subroutine', sub.name), '(', self.cmd('sloppy') ]) if sub.parameters: params = ", ".join(map(lambda s: self.cmd('textbf', s), sub.parameters)) f.writelines([params]) f.writelines([')}\n\n'])	def write_subroutine(self, sub, f): f.writelines([ r'\begin{subroutinedef}{', self.cmd('subroutine', sub.name), '(', self.cmd('sloppy') ]) if sub.parameters: params = ", ".join(map(lambda s: self.cmd('textbf', s), sub.parameters)) f.writelines([params]) f.writelines([')}\n\n'])	480,517
def write_subroutine(self, sub, f): f.writelines([ r'\begin{subroutinedef}{', self.cmd('subroutine', sub.name), '(', self.cmd('sloppy') ]) if sub.parameters: params = ", ".join(map(lambda s: self.cmd('textbf', s), sub.parameters)) f.writelines([params]) f.writelines([')}\n\n'])	def write_subroutine(self, sub, f): f.writelines([ r'\begin{subroutinedef}{', self.cmd('subroutine', sub.name), '(', self.cmd('sloppy') ]) if sub.parameters: params = ", ".join(map(lambda s: self.cmd('textbf', s), sub.parameters)) f.writelines([params]) f.writelines([')}\n\n'])	480,518
def test_abundance_dist(self): dist = self.kh.abundance_distribution() assert dist[0] == 4**4 assert sum(dist[1:]) == 0 n = self.kh.consume('AAAA') n = self.kh.consume('AACT') dist = self.kh.abundance_distribution() assert sum(dist[1:]) == 2 assert dist[1] == 2	def test_abundance_dist(self): dist = self.kh.abundance_distribution() assert dist[0] == 4**4 assert sum(dist[1:]) == 0 n = self.kh.consume('AAAA') n = self.kh.consume('AACT') dist = self.kh.abundance_distribution() assert sum(dist[1:]) == 2, dist assert dist[1] == 2	480,519
def main(): global done, worker_count done = False worker_count = 0 infile = sys.argv[1] outfile = infile + '.graphsize2' print 'creating ht' ht = khmer.new_hashbits(K, HASHTABLE_SIZE, 1) print 'eating fa', infile total_reads, n_consumed = ht.consume_fasta(infile) outfp = open(outfile, 'w') inqueue = Queue.Queue(50)...	def main(): global done, worker_count done = False worker_count = 0 infile = sys.argv[1] outfile = infile + '.graphsize' print 'creating ht' ht = khmer.new_hashbits(K, HASHTABLE_SIZE, 1) print 'eating fa', infile total_reads, n_consumed = ht.consume_fasta(infile) outfp = open(outfile, 'w') inqueue = Queue.Queue(50) ...	480,520
def test_3_merge_013(self): ht = khmer.new_hashbits(20, 4**14+1) filename = os.path.join(thisdir, 'test-graph2.fa')	def test_3_merge_013(self): ht = khmer.new_hashbits(20, 4**14+1) filename = os.path.join(thisdir, 'test-graph2.fa')	480,521
def test_3_merge_023(self): ht = khmer.new_hashbits(20, 4**14+1) filename = os.path.join(thisdir, 'test-graph2.fa')	def test_3_merge_023(self): ht = khmer.new_hashbits(20, 4**14+1) filename = os.path.join(thisdir, 'test-graph2.fa')	480,522
def test_random_20_a_succ(self): ht = khmer.new_hashbits(20, 4**13+1) filename = os.path.join(thisdir, 'test-data/random-20-a.fa') outfile = filename + '.out'	def test_random_20_a_succ(self): ht = khmer.new_hashbits(20, 4**13+1) filename = os.path.join(thisdir, 'test-data/random-20-a.fa') outfile = filename + '.out'	480,523
def test_random_20_a_succ_II(self): ht = khmer.new_hashbits(20, 4**13+1) filename = os.path.join(thisdir, 'test-data/random-20-a.fa') outfile = filename + '.out'	def test_random_20_a_succ_II(self): ht = khmer.new_hashbits(20, 4**13+1) filename = os.path.join(thisdir, 'test-data/random-20-a.fa') outfile = filename + '.out'	480,524
def test_random_20_a_succ_III(self): ht = khmer.new_hashbits(20, 4**13+1) filename = os.path.join(thisdir, 'test-data/random-20-a.fa') outfile = filename + '.out'	def test_random_20_a_succ_III(self): ht = khmer.new_hashbits(20, 4**13+1) filename = os.path.join(thisdir, 'test-data/random-20-a.fa') outfile = filename + '.out'	480,525
def test_save_load_merge(self): ht = khmer.new_hashbits(20, 4**14+1) filename = os.path.join(thisdir, 'test-graph2.fa')	def test_save_load_merge(self): ht = khmer.new_hashbits(20, 4**14+1) filename = os.path.join(thisdir, 'test-graph2.fa')	480,526
def test_complex6_32_12(self): ht = khmer.new_hashtable(20, 4**12+1)	def test_complex6_32_12(self): ht = khmer.new_hashtable(20, 4**12+1)	480,527
def test_complex6_32_12(self): ht = khmer.new_hashtable(20, 4**12+1)	def test_complex6_32_12(self): ht = khmer.new_hashtable(20, 4**12+1)	480,528
def main(dir1, dir2, n_threads): # detect all of the relevant partitionmap files subset_filenames = glob.glob(os.path.join(dir1, '*.pmap')) # create empty hashtable structure ht = khmer.new_hashtable(K, 1) # put jobs on queue merge_queue = Queue.Queue() for filename in subset_filenames: merge_queue.put((ht, filename)...	def main(dir1, dir2, n_threads): # detect all of the relevant partitionmap files subset_filenames = glob.glob(os.path.join(dir1, '*.pmap')) # create empty hashtable structure ht = khmer.new_hashbits(K, 1, 1) # put jobs on queue merge_queue = Queue.Queue() for filename in subset_filenames: merge_queue.put((ht, filenam...	480,529
def read_partition_file(fp): for n, line in enumerate(fp): if n % 2 == 0: surrendered = False name, partition_id = line[1:].strip().rsplit('\t', 1) if '*' in partition_id: partition_id = int(partition_id[:-1]) surrendered = True else: partition_id = int(partition_id) else: sequence = line.strip() yield name, partitio...	def read_partition_file(fp): for n, line in enumerate(fp): if n % 2 == 0: surrendered = False name, partition_id = line[1:].strip().rsplit('\t', 1) if '*' in partition_id: partition_id = int(partition_id[:-1]) surrendered = True else: partition_id = int(partition_id) else: sequence = line.strip() yield name, partitio...	480,530
def main(dir1, dir2, n_threads): # detect all of the relevant partitionmap files subset_filenames = glob.glob(os.path.join(dir1, '*.pmap')) # put on queue merge_queue = Queue.Queue() for filename in subset_filenames: merge_queue.put((ht, filename)) print 'starting threads' threads = [] for n in range(n_threads): t =...	def ht = khmer.new_hashtable(K, 1) main(dir1, ht = khmer.new_hashtable(K, 1) dir2, ht = khmer.new_hashtable(K, 1) n_threads): ht = khmer.new_hashtable(K, 1) # ht = khmer.new_hashtable(K, 1) detect ht = khmer.new_hashtable(K, 1) all ht = khmer.new_hashtable(K, 1) of ht = khmer.new_hashtable(K, 1) the ht ...	480,531
def test_random_20_a_succ_III(self): ht = khmer.new_hashbits(20, 4**13+1) filename = os.path.join(thisdir, 'test-data/random-20-a.fa') outfile = filename + '.out'	def test_random_20_a_succ_III(self): ht = khmer.new_hashbits(20, 4**13+1) filename = os.path.join(thisdir, 'test-data/random-20-a.fa') outfile = filename + '.out'	480,532
def test_surrendered(self): ht = khmer.new_hashtable(32, 4**15+1)	def test_surrendered(self): ht = khmer.new_hashtable(32, 4**15+1)	480,533
def read_partition_file(fp): for n, line in enumerate(fp): if n % 2 == 0: surrendered = False name, partition_id = line[1:].strip().split('\t') if '*' in partition_id: partition_id = int(partition_id[:-1]) surrendered = True else: partition_id = int(partition_id) else: sequence = line.strip() yield name, partition_id...	def read_partition_file(fp): for n, line in enumerate(fp): if n % 2 == 0: surrendered = False name, partition_id = line[1:].strip().rsplit('\t', 1) if '*' in partition_id: partition_id = int(partition_id[:-1]) surrendered = True else: partition_id = int(partition_id) else: sequence = line.strip() yield name, partitio...	480,534
def read_partition_file(fp): for n, line in enumerate(fp): if n % 2 == 0: surrendered = False name, partition_id = line[1:].strip().split('\t') if '*' in partition_id: partition_id = int(partition_id[:-1]) surrendered = True else: partition_id = int(partition_id) else: sequence = line.strip() yield name, partition_id...	def read_partition_file(fp): for n, line in enumerate(fp): if n % 2 == 0: surrendered = False name, partition_id = line[1:].strip().split('\t') if '*' in partition_id: partition_id = int(partition_id[:-1]) surrendered = True else: partition_id = int(partition_id) else: sequence = line.strip() yield name, partition_id...	480,535
def read_partition_file(fp): for n, line in enumerate(fp): if n % 2 == 0: surrendered = False name, partition_id = line[1:].strip().split('\t') if '*' in partition_id: partition_id = int(partition_id[:-1]) surrendered = True else: partition_id = int(partition_id) else: sequence = line.strip() yield name, partition_id...	def read_partition_file(fp): for n, line in enumerate(fp): if n % 2 == 0: surrendered = False name, partition_id = line[1:].strip().split('\t') if '*' in partition_id: partition_id = int(partition_id[:-1]) surrendered = True else: partition_id = int(partition_id) else: sequence = line.strip() yield name, partition_id...	480,536
def read_partition_file(fp): for n, line in enumerate(fp): if n % 2 == 0: surrendered = False name, partition_id = line[1:].strip().split('\t') if '*' in partition_id: partition_id = int(partition_id[:-1]) surrendered = True else: partition_id = int(partition_id) else: sequence = line.strip() yield name, partition_id...	def read_partition_file(fp): for n, line in enumerate(fp): if n % 2 == 0: surrendered = False name, partition_id = line[1:].strip().split('\t') if '*' in partition_id: partition_id = int(partition_id[:-1]) surrendered = True else: partition_id = int(partition_id) else: sequence = line.strip() yield name, partition_id...	480,537
def threaded_calc(ht, filename, start, stop): x = ht.do_subset_partition(filename, start, stop) print 'done!' results.append(x)	def threaded_calc(ht, start, stop): x = ht.do_subset_partition(start, stop) print 'done!' results.append(x)	480,538
def threaded_calc(ht, filename, start, stop): x = ht.do_subset_partition(filename, start, stop) print 'done!' results.append(x)	defthreaded_calc(ht,filename,start,stop):x=ht.do_subset_partition(filename,start,stop)print'done!'results.append(x)	480,539