sequence stringlengths 546 16.2k | code stringlengths 108 19.3k |
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0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:gather_categories; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:imap; 5, identifier:header; 6, default_parameter; 6, 7; 6, 8; 7, identifier:categories; 8, None; 9, block; 9, 10; 9, 12; 9, 13; 9, 34; 9, 55; 9, 61; 9, 68; 9, 127; 9, 128; 9, 151... | def gather_categories(imap, header, categories=None):
"""
Find the user specified categories in the map and create a dictionary to contain the
relevant data for each type within the categories. Multiple categories will have their
types combined such that each possible combination will have its own entry... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 10; 2, function_name:color_mapping; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:sample_map; 5, identifier:header; 6, identifier:group_column; 7, default_parameter; 7, 8; 7, 9; 8, identifier:color_column; 9, None; 10, block; 10, 11; 10, 13; 10, 19; 10, 29;... | def color_mapping(sample_map, header, group_column, color_column=None):
"""
Determine color-category mapping. If color_column was specified, then map the category
names to color values. Otherwise, use the palettable colors to automatically generate
a set of colors for the group values.
:type sample... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 29; 2, function_name:shuffle_genome; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 12; 3, 15; 3, 16; 3, 19; 3, 22; 3, 23; 3, 26; 4, identifier:genome; 5, identifier:cat; 6, default_parameter; 6, 7; 6, 8; 7, identifier:fraction; 8, call; 8, 9; 8, 10; 9, identifier:float; 10,... | def shuffle_genome(genome, cat, fraction = float(100), plot = True, \
alpha = 0.1, beta = 100000, \
min_length = 1000, max_length = 200000):
"""
randomly shuffle genome
"""
header = '>randomized_%s' % (genome.name)
sequence = list(''.join([i[1] for i in parse_fasta(genome)]))
len... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:sam2fastq; 3, parameters; 3, 4; 3, 5; 3, 8; 4, identifier:sam; 5, default_parameter; 5, 6; 5, 7; 6, identifier:singles; 7, False; 8, default_parameter; 8, 9; 8, 10; 9, identifier:force; 10, False; 11, block; 11, 12; 11, 14; 11, 22; 12, express... | def sam2fastq(sam, singles = False, force = False):
"""
convert sam to fastq
"""
L, R = None, None
for line in sam:
if line.startswith('@') is True:
continue
line = line.strip().split()
bit = [True if i == '1' else False \
for i in bin(int(line[1])... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:sort_sam; 3, parameters; 3, 4; 3, 5; 4, identifier:sam; 5, identifier:sort; 6, block; 6, 7; 6, 9; 6, 31; 6, 143; 7, expression_statement; 7, 8; 8, comment; 9, expression_statement; 9, 10; 10, assignment; 10, 11; 10, 12; 11, identifier:tempdir; ... | def sort_sam(sam, sort):
"""
sort sam file
"""
tempdir = '%s/' % (os.path.abspath(sam).rsplit('/', 1)[0])
if sort is True:
mapping = '%s.sorted.sam' % (sam.rsplit('.', 1)[0])
if sam != '-':
if os.path.exists(mapping) is False:
os.system("\
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 12; 2, function_name:crossmap; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 8; 3, 9; 3, 10; 3, 11; 4, identifier:fas; 5, identifier:reads; 6, identifier:options; 7, identifier:no_shrink; 8, identifier:keepDB; 9, identifier:threads; 10, identifier:cluster; 11, identif... | def crossmap(fas, reads, options, no_shrink, keepDB, threads, cluster, nodes):
"""
map all read sets against all fasta files
"""
if cluster is True:
threads = '48'
btc = []
for fa in fas:
btd = bowtiedb(fa, keepDB)
F, R, U = reads
if F is not False:
if... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:bit_by_bit; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:in_data; 6, block; 6, 7; 6, 9; 6, 10; 6, 28; 6, 34; 6, 100; 6, 138; 6, 155; 7, expression_statement; 7, 8; 8, comment; 9, comment; 10, if_statement; 10, 11; 10, 16; 11, ca... | def bit_by_bit(self, in_data):
"""
Classic simple and slow CRC implementation. This function iterates bit
by bit over the augmented input message and returns the calculated CRC
value at the end.
"""
# If the input data is a string, convert to bytes.
if isinstance... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:parse_ggKbase_tables; 3, parameters; 3, 4; 3, 5; 4, identifier:tables; 5, identifier:id_type; 6, block; 6, 7; 6, 9; 6, 13; 6, 282; 7, expression_statement; 7, 8; 8, comment; 9, expression_statement; 9, 10; 10, assignment; 10, 11; 10, 12; 11, id... | def parse_ggKbase_tables(tables, id_type):
"""
convert ggKbase genome info tables to dictionary
"""
g2info = {}
for table in tables:
for line in open(table):
line = line.strip().split('\t')
if line[0].startswith('name'):
header = line
h... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:top_hits; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:hits; 5, identifier:num; 6, identifier:column; 7, identifier:reverse; 8, block; 8, 9; 8, 11; 8, 26; 9, expression_statement; 9, 10; 10, comment; 11, expression_statement; 11, 12; 12... | def top_hits(hits, num, column, reverse):
"""
get top hits after sorting by column number
"""
hits.sort(key = itemgetter(column), reverse = reverse)
for hit in hits[0:num]:
yield hit |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:numBlast_sort; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 4, identifier:blast; 5, identifier:numHits; 6, identifier:evalueT; 7, identifier:bitT; 8, block; 8, 9; 8, 11; 8, 27; 8, 30; 8, 40; 8, 140; 8, 149; 9, expression_statement; 9, 10; 10, comment... | def numBlast_sort(blast, numHits, evalueT, bitT):
"""
parse b6 output with sorting
"""
header = ['#query', 'target', 'pident', 'alen', 'mismatch', 'gapopen',
'qstart', 'qend', 'tstart', 'tend', 'evalue', 'bitscore']
yield header
hmm = {h:[] for h in header}
for line in blast:
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:numDomtblout; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 8; 4, identifier:domtblout; 5, identifier:numHits; 6, identifier:evalueT; 7, identifier:bitT; 8, identifier:sort; 9, block; 9, 10; 9, 12; 9, 31; 9, 58; 9, 61; 9, 69; 9, 280; 10, expression... | def numDomtblout(domtblout, numHits, evalueT, bitT, sort):
"""
parse hmm domain table output
this version is faster but does not work unless the table is sorted
"""
if sort is True:
for hit in numDomtblout_sort(domtblout, numHits, evalueT, bitT):
yield hit
return
head... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:compare_clades; 3, parameters; 3, 4; 4, identifier:pw; 5, block; 5, 6; 5, 8; 5, 22; 6, expression_statement; 6, 7; 7, comment; 8, expression_statement; 8, 9; 9, assignment; 9, 10; 9, 11; 10, identifier:names; 11, call; 11, 12; 11, 13; 12, ident... | def compare_clades(pw):
"""
print min. pident within each clade and then matrix of between-clade max.
"""
names = sorted(set([i for i in pw]))
for i in range(0, 4):
wi, bt = {}, {}
for a in names:
for b in pw[a]:
if ';' not in a or ';' not in b:
... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:searchAccession; 3, parameters; 3, 4; 4, identifier:acc; 5, block; 5, 6; 5, 8; 5, 9; 5, 10; 5, 20; 5, 95; 5, 96; 5, 106; 5, 181; 5, 182; 5, 192; 5, 267; 5, 298; 6, expression_statement; 6, 7; 7, comment; 8, comment; 9, comment; 10, expression_s... | def searchAccession(acc):
"""
attempt to use NCBI Entrez to get
BioSample ID
"""
# try genbank file
# genome database
out, error = entrez('genome', acc)
for line in out.splitlines():
line = line.decode('ascii').strip()
if 'Assembly_Accession' in line or 'BioSample' in lin... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 11; 2, function_name:_configure_logger; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 8; 3, 9; 3, 10; 4, identifier:fmt; 5, identifier:quiet; 6, identifier:level; 7, identifier:fpath; 8, identifier:pre_hooks; 9, identifier:post_hooks; 10, identifier:metric_grouping_in... | def _configure_logger(fmt, quiet, level, fpath,
pre_hooks, post_hooks, metric_grouping_interval):
"""
configures a logger when required write to stderr or a file
"""
# NOTE not thread safe. Multiple BaseScripts cannot be instantiated concurrently.
level = getattr(logging, level.upper())
gl... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:combine_modifiers; 3, parameters; 3, 4; 3, 5; 4, identifier:self; 5, identifier:graphemes; 6, block; 6, 7; 6, 9; 6, 13; 6, 17; 6, 24; 6, 210; 6, 211; 6, 221; 6, 225; 6, 229; 6, 287; 7, expression_statement; 7, 8; 8, comment; 9, expression_state... | def combine_modifiers(self, graphemes):
"""
Given a string that is space-delimited on Unicode grapheme clusters,
group Unicode modifier letters with their preceding base characters,
deal with tie bars, etc.
Parameters
----------
string : str
A Unicode... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 9; 2, function_name:check_mismatches; 3, parameters; 3, 4; 3, 5; 3, 6; 3, 7; 3, 8; 4, identifier:read; 5, identifier:pair; 6, identifier:mismatches; 7, identifier:mm_option; 8, identifier:req_map; 9, block; 9, 10; 9, 12; 9, 13; 9, 48; 9, 49; 9, 56; 9, 63; 9, 64; 9... | def check_mismatches(read, pair, mismatches, mm_option, req_map):
"""
- check to see if the read maps with <= threshold number of mismatches
- mm_option = 'one' or 'both' depending on whether or not one or both reads
in a pair need to pass the mismatch threshold
- pair can be False if read does n... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 4; 2, function_name:get_steam; 3, parameters; 4, block; 4, 5; 4, 7; 4, 8; 4, 9; 4, 10; 4, 30; 4, 31; 4, 32; 4, 40; 4, 54; 4, 68; 4, 69; 4, 70; 4, 71; 4, 72; 4, 97; 4, 98; 4, 99; 4, 100; 4, 101; 5, expression_statement; 5, 6; 6, comment; 7, comment; 8, comment; 9, ... | def get_steam():
"""
Returns a Steam object representing the current Steam installation on the
users computer. If the user doesn't have Steam installed, returns None.
"""
# Helper function which checks if the potential userdata directory exists
# and returns a new Steam instance with that userdata directory... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 8; 2, function_name:generate_barcodes; 3, parameters; 3, 4; 3, 5; 4, identifier:nIds; 5, default_parameter; 5, 6; 5, 7; 6, identifier:codeLen; 7, integer:12; 8, block; 8, 9; 8, 11; 8, 41; 8, 56; 8, 77; 8, 78; 8, 90; 8, 115; 8, 119; 8, 195; 9, expression_statement;... | def generate_barcodes(nIds, codeLen=12):
"""
Given a list of sample IDs generate unique n-base barcodes for each.
Note that only 4^n unique barcodes are possible.
"""
def next_code(b, c, i):
return c[:i] + b + (c[i+1:] if i < -1 else '')
def rand_base():
return random.choice(['A... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 7; 2, function_name:parse_fasta_annotations; 3, parameters; 3, 4; 3, 5; 3, 6; 4, identifier:fastas; 5, identifier:annot_tables; 6, identifier:trans_table; 7, block; 7, 8; 7, 10; 7, 58; 8, expression_statement; 8, 9; 9, comment; 10, if_statement; 10, 11; 10, 14; 11... | def parse_fasta_annotations(fastas, annot_tables, trans_table):
"""
parse gene call information from Prodigal fasta output
"""
if annot_tables is not False:
annots = {}
for table in annot_tables:
for cds in open(table):
ID, start, end, strand = cds.strip().spl... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:find_consensus; 3, parameters; 3, 4; 4, identifier:bases; 5, block; 5, 6; 5, 8; 5, 17; 5, 34; 5, 35; 5, 78; 5, 96; 5, 126; 5, 186; 5, 192; 5, 198; 6, expression_statement; 6, 7; 7, comment; 8, expression_statement; 8, 9; 9, assignment; 9, 10; 9... | def find_consensus(bases):
"""
find consensus base based on nucleotide
frequencies
"""
nucs = ['A', 'T', 'G', 'C', 'N']
total = sum([bases[nuc] for nuc in nucs if nuc in bases])
# save most common base as consensus (random nuc if there is a tie)
try:
top = max([bases[nuc] for nuc... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 5; 2, function_name:print_consensus; 3, parameters; 3, 4; 4, identifier:genomes; 5, block; 5, 6; 5, 8; 5, 9; 5, 13; 5, 14; 5, 132; 5, 133; 5, 209; 6, expression_statement; 6, 7; 7, comment; 8, comment; 9, expression_statement; 9, 10; 10, assignment; 10, 11; 10, 12... | def print_consensus(genomes):
"""
print consensensus sequences for each genome and sample
"""
# generate consensus sequences
cons = {} # cons[genome][sample][contig] = consensus
for genome, contigs in list(genomes.items()):
cons[genome] = {}
for contig, samples in list(contigs.it... |
0, module; 0, 1; 1, function_definition; 1, 2; 1, 3; 1, 6; 2, function_name:parse_cov; 3, parameters; 3, 4; 3, 5; 4, identifier:cov_table; 5, identifier:scaffold2genome; 6, block; 6, 7; 6, 9; 6, 13; 6, 14; 6, 18; 6, 19; 6, 20; 6, 190; 6, 191; 6, 207; 6, 267; 7, expression_statement; 7, 8; 8, comment; 9, expression_stat... | def parse_cov(cov_table, scaffold2genome):
"""
calculate genome coverage from scaffold coverage table
"""
size = {} # size[genome] = genome size
mapped = {} # mapped[genome][sample] = mapped bases
# parse coverage files
for line in open(cov_table):
line = line.strip().split('\t')
... |
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