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flo-compbio/genometools | genometools/expression/matrix.py | ExpMatrix.write_tsv | def write_tsv(self, file_path: str, encoding: str = 'UTF-8',
sep: str = '\t'):
"""Write expression matrix to a tab-delimited text file.
Parameters
----------
file_path: str
The path of the output file.
encoding: str, optional
The file en... | python | def write_tsv(self, file_path: str, encoding: str = 'UTF-8',
sep: str = '\t'):
"""Write expression matrix to a tab-delimited text file.
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The path of the output file.
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flo-compbio/genometools | genometools/expression/matrix.py | ExpMatrix.write_sparse | def write_sparse(self, file_path: str):
"""Write a sparse representation to a tab-delimited text file.
TODO: docstring"""
coo = sparse.coo_matrix(self.X)
data = OrderedDict([(0, coo.row+1), (1, coo.col+1), (2, coo.data)])
df = pd.DataFrame(data, columns=data.keys())
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"""Write a sparse representation to a tab-delimited text file.
TODO: docstring"""
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flo-compbio/genometools | genometools/expression/matrix.py | ExpMatrix.read_sparse | def read_sparse(cls, file_path: str):
"""Read a sparse representation from a tab-delimited text file.
TODO: docstring"""
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"""Read a sparse representation from a tab-delimited text file.
TODO: docstring"""
with open(file_path) as fh:
next(fh) # skip header line
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flo-compbio/genometools | genometools/expression/matrix.py | ExpMatrix.read_10xgenomics | def read_10xgenomics(cls, tarball_fpath: str, prefix: str,
use_ensembl_ids: bool = False):
"""Read a 10X genomics compressed tarball containing expression data.
Note: common prefix patterns:
- "filtered_gene_bc_matrices/[annotations]/"
- "filtered_matric... | python | def read_10xgenomics(cls, tarball_fpath: str, prefix: str,
use_ensembl_ids: bool = False):
"""Read a 10X genomics compressed tarball containing expression data.
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flo-compbio/genometools | genometools/expression/convert_entrez2gene.py | get_argument_parser | def get_argument_parser():
"""Function to obtain the argument parser.
Parameters
----------
Returns
-------
`argparse.ArgumentParser`
A fully configured `argparse.ArgumentParser` object.
Notes
-----
This function can also be used by the `sphinx-argparse` extension for
... | python | def get_argument_parser():
"""Function to obtain the argument parser.
Parameters
----------
Returns
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`argparse.ArgumentParser`
A fully configured `argparse.ArgumentParser` object.
Notes
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This function can also be used by the `sphinx-argparse` extension for
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jvsteiner/merkletree | merkle.py | check_chain | def check_chain(chain):
"""Verify a merkle chain to see if the Merkle root can be reproduced.
"""
link = chain[0][0]
for i in range(1, len(chain) - 1):
if chain[i][1] == 'R':
link = hash_function(link + chain[i][0]).digest()
elif chain[i][1] == 'L':
link = hash_fu... | python | def check_chain(chain):
"""Verify a merkle chain to see if the Merkle root can be reproduced.
"""
link = chain[0][0]
for i in range(1, len(chain) - 1):
if chain[i][1] == 'R':
link = hash_function(link + chain[i][0]).digest()
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jvsteiner/merkletree | merkle.py | check_hex_chain | def check_hex_chain(chain):
"""Verify a merkle chain, with hashes hex encoded, to see if the Merkle root can be reproduced.
"""
return codecs.encode(check_chain([(codecs.decode(i[0], 'hex_codec'), i[1]) for i in chain]), 'hex_codec') | python | def check_hex_chain(chain):
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jvsteiner/merkletree | merkle.py | MerkleTree.add_hash | def add_hash(self, value):
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"""
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jvsteiner/merkletree | merkle.py | MerkleTree.clear | def clear(self):
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jvsteiner/merkletree | merkle.py | MerkleTree.build_fun | def build_fun(self, layer=None):
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jvsteiner/merkletree | merkle.py | MerkleTree._build | def _build(self, leaves):
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jvsteiner/merkletree | merkle.py | MerkleTree.get_chain | def get_chain(self, index):
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jvsteiner/merkletree | merkle.py | MerkleTree.get_all_chains | def get_all_chains(self):
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jvsteiner/merkletree | merkle.py | MerkleTree.get_hex_chain | def get_hex_chain(self, index):
"""Assemble and return the chain leading from a given node to the merkle root of this tree
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jvsteiner/merkletree | merkle.py | MerkleTree.get_all_hex_chains | def get_all_hex_chains(self):
"""Assemble and return a list of all chains for all nodes to the merkle root, hex encoded.
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jvsteiner/merkletree | merkle.py | MerkleTree._get_whole_subtrees | def _get_whole_subtrees(self):
"""Returns an array of nodes in the tree that have balanced subtrees beneath them,
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"""
subtrees = []
loose_leaves = len(self.leaves) - 2**int(log(len(self.leaves), 2))
the_node = self.root
while loose_leave... | python | def _get_whole_subtrees(self):
"""Returns an array of nodes in the tree that have balanced subtrees beneath them,
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subtrees = []
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"""Add a new leaf, and adjust the tree, without rebuilding the whole thing.
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flo-compbio/genometools | genometools/enrichment/result.py | StaticGSEResult.fold_enrichment | def fold_enrichment(self):
"""Returns the fold enrichment of the gene set.
Fold enrichment is defined as ratio between the observed and the
expected number of gene set genes present.
"""
expected = self.K * (self.n/float(self.N))
return self.k / expected | python | def fold_enrichment(self):
"""Returns the fold enrichment of the gene set.
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"""
expected = self.K * (self.n/float(self.N))
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The maximum length of the gene set name (in characters). If the
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acorg/dark-matter | bin/get-reads.py | main | def main(recordFilenames, fastaFilename, title, xRange, bitRange):
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Print reads that match in a specified X-axis and bit score range.
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Print reads that match in a specified X-axis and bit score range.
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biocommons/bioutils | src/bioutils/seqfetcher.py | fetch_seq | def fetch_seq(ac, start_i=None, end_i=None):
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:param string ac: accession of sequence to fetch
:param int start_i: start position of *interbase* interval
:param int end_i: end position of *interbase* interval
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biocommons/bioutils | src/bioutils/seqfetcher.py | _fetch_seq_ncbi | def _fetch_seq_ncbi(ac, start_i=None, end_i=None):
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chro... | python | def _fetch_seq_ncbi(ac, start_i=None, end_i=None):
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biocommons/bioutils | src/bioutils/seqfetcher.py | _add_eutils_api_key | def _add_eutils_api_key(url):
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"""
apikey = os.environ.get("NCBI_API_KEY")
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url += "&api_k... | python | def _add_eutils_api_key(url):
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nkavaldj/myhdl_lib | myhdl_lib/mem.py | rom | def rom(addr, dout, CONTENT):
''' CONTENT == tuple of non-sparse values '''
@always_comb
def read():
dout.next = CONTENT[int(addr)]
return read | python | def rom(addr, dout, CONTENT):
''' CONTENT == tuple of non-sparse values '''
@always_comb
def read():
dout.next = CONTENT[int(addr)]
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nkavaldj/myhdl_lib | myhdl_lib/mem.py | ram_sp_ar | def ram_sp_ar(clk, we, addr, di, do):
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memL = [Signal(intbv(0)[len(di):]) for _ in range(2**len(addr))]
@always(clk.posedge)
def write():
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def read():
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... | python | def ram_sp_ar(clk, we, addr, di, do):
''' RAM: Single-Port, Asynchronous Read '''
memL = [Signal(intbv(0)[len(di):]) for _ in range(2**len(addr))]
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nkavaldj/myhdl_lib | myhdl_lib/mem.py | ram_sdp_rf | def ram_sdp_rf(clk, we, addrw, addrr, di, do):
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memL = [Signal(intbv(0)[len(di):]) for _ in range(2**len(addrr))]
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nkavaldj/myhdl_lib | myhdl_lib/mem.py | ram_dp_rf | def ram_dp_rf(clka, clkb, wea, web, addra, addrb, dia, dib, doa, dob):
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nkavaldj/myhdl_lib | myhdl_lib/mem.py | convert_rom | def convert_rom(ADDR_WIDTH=8, DATA_WIDTH=8, CONTENT=(4,5,6,7)):
''' Convert ROM'''
addr = Signal(intbv(0)[ADDR_WIDTH:])
dout = Signal(intbv(0)[DATA_WIDTH:])
toVerilog(rom, addr, dout, CONTENT) | python | def convert_rom(ADDR_WIDTH=8, DATA_WIDTH=8, CONTENT=(4,5,6,7)):
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addr = Signal(intbv(0)[ADDR_WIDTH:])
dout = Signal(intbv(0)[DATA_WIDTH:])
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nkavaldj/myhdl_lib | myhdl_lib/mem.py | convert_ram_sp_rf | def convert_ram_sp_rf(ADDR_WIDTH=8, DATA_WIDTH=8):
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toVerilog(ram_sp_rf, clk, we, addr, di, do) | python | def convert_ram_sp_rf(ADDR_WIDTH=8, DATA_WIDTH=8):
''' Convert RAM: Single-Port, Read-First '''
clk = Signal(bool(0))
we = Signal(bool(0))
addr = Signal(intbv(0)[ADDR_WIDTH:])
di = Signal(intbv(0)[DATA_WIDTH:])
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nkavaldj/myhdl_lib | myhdl_lib/mem.py | convert_ram_sp_wf | def convert_ram_sp_wf(ADDR_WIDTH=8, DATA_WIDTH=8):
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clk = Signal(bool(0))
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''' Convert RAM: Single-Port, Write-First '''
clk = Signal(bool(0))
we = Signal(bool(0))
addr = Signal(intbv(0)[ADDR_WIDTH:])
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nkavaldj/myhdl_lib | myhdl_lib/mem.py | convert_ram_sp_ar | def convert_ram_sp_ar(ADDR_WIDTH=8, DATA_WIDTH=8):
''' Convert RAM: Single-Port, Asynchronous Read '''
clk = Signal(bool(0))
we = Signal(bool(0))
addr = Signal(intbv(0)[ADDR_WIDTH:])
di = Signal(intbv(0)[DATA_WIDTH:])
do = Signal(intbv(0)[DATA_WIDTH:])
toVerilog(ram_sp_ar, clk, we, addr, di,... | python | def convert_ram_sp_ar(ADDR_WIDTH=8, DATA_WIDTH=8):
''' Convert RAM: Single-Port, Asynchronous Read '''
clk = Signal(bool(0))
we = Signal(bool(0))
addr = Signal(intbv(0)[ADDR_WIDTH:])
di = Signal(intbv(0)[DATA_WIDTH:])
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nkavaldj/myhdl_lib | myhdl_lib/mem.py | convert_ram_sdp_rf | def convert_ram_sdp_rf(ADDR_WIDTH=8, DATA_WIDTH=8):
''' Convert RAM: Simple-Dual-Port, Read-First '''
clk = Signal(bool(0))
we = Signal(bool(0))
addrw = Signal(intbv(0)[ADDR_WIDTH:])
addrr = Signal(intbv(0)[ADDR_WIDTH:])
di = Signal(intbv(0)[DATA_WIDTH:])
do = Signal(intbv(0)[DATA_WIDTH:])
... | python | def convert_ram_sdp_rf(ADDR_WIDTH=8, DATA_WIDTH=8):
''' Convert RAM: Simple-Dual-Port, Read-First '''
clk = Signal(bool(0))
we = Signal(bool(0))
addrw = Signal(intbv(0)[ADDR_WIDTH:])
addrr = Signal(intbv(0)[ADDR_WIDTH:])
di = Signal(intbv(0)[DATA_WIDTH:])
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nkavaldj/myhdl_lib | myhdl_lib/mem.py | convert_ram_sdp_wf | def convert_ram_sdp_wf(ADDR_WIDTH=8, DATA_WIDTH=8):
''' Convert RAM: Simple-Dual-Port, Write-First '''
clk = Signal(bool(0))
we = Signal(bool(0))
addrw = Signal(intbv(0)[ADDR_WIDTH:])
addrr = Signal(intbv(0)[ADDR_WIDTH:])
di = Signal(intbv(0)[DATA_WIDTH:])
do = Signal(intbv(0)[DATA_WIDTH:])
... | python | def convert_ram_sdp_wf(ADDR_WIDTH=8, DATA_WIDTH=8):
''' Convert RAM: Simple-Dual-Port, Write-First '''
clk = Signal(bool(0))
we = Signal(bool(0))
addrw = Signal(intbv(0)[ADDR_WIDTH:])
addrr = Signal(intbv(0)[ADDR_WIDTH:])
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nkavaldj/myhdl_lib | myhdl_lib/mem.py | convert_ram_sdp_ar | def convert_ram_sdp_ar(ADDR_WIDTH=8, DATA_WIDTH=8):
''' Convert RAM: Simple-Dual-Port, Asynchronous Read'''
clk = Signal(bool(0))
we = Signal(bool(0))
addrw = Signal(intbv(0)[ADDR_WIDTH:])
addrr = Signal(intbv(0)[ADDR_WIDTH:])
di = Signal(intbv(0)[DATA_WIDTH:])
do = Signal(intbv(0)[DATA_WIDT... | python | def convert_ram_sdp_ar(ADDR_WIDTH=8, DATA_WIDTH=8):
''' Convert RAM: Simple-Dual-Port, Asynchronous Read'''
clk = Signal(bool(0))
we = Signal(bool(0))
addrw = Signal(intbv(0)[ADDR_WIDTH:])
addrr = Signal(intbv(0)[ADDR_WIDTH:])
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nkavaldj/myhdl_lib | myhdl_lib/mem.py | convert_ram_dp_ar | def convert_ram_dp_ar(ADDR_WIDTH=8, DATA_WIDTH=8):
''' Convert RAM: Dual-Port, Asynchronous Read '''
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clkb = Signal(bool(0))
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web = Signal(bool(0))
addra = Signal(intbv(0)[ADDR_WIDTH:])
addrb = Signal(intbv(0)[ADDR_WIDTH:])
dia = Signal(intbv(0)... | python | def convert_ram_dp_ar(ADDR_WIDTH=8, DATA_WIDTH=8):
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clka = Signal(bool(0))
clkb = Signal(bool(0))
wea = Signal(bool(0))
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addra = Signal(intbv(0)[ADDR_WIDTH:])
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disqus/overseer | overseer/models.py | Event.post_to_twitter | def post_to_twitter(self, message=None):
"""Update twitter status, i.e., post a tweet"""
consumer = oauth2.Consumer(key=conf.TWITTER_CONSUMER_KEY,
secret=conf.TWITTER_CONSUMER_SECRET)
token = oauth2.Token(key=conf.TWITTER_ACCESS_TOKEN, secret=conf.TWITTER_ACCES... | python | def post_to_twitter(self, message=None):
"""Update twitter status, i.e., post a tweet"""
consumer = oauth2.Consumer(key=conf.TWITTER_CONSUMER_KEY,
secret=conf.TWITTER_CONSUMER_SECRET)
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flo-compbio/genometools | genometools/ebi/uniprot_goa.py | get_gaf_gene_ontology_file | def get_gaf_gene_ontology_file(path):
"""Extract the gene ontology file associated with a GO annotation file.
Parameters
----------
path: str
The path name of the GO annotation file.
Returns
-------
str
The URL of the associated gene ontology file.
"""
assert isinst... | python | def get_gaf_gene_ontology_file(path):
"""Extract the gene ontology file associated with a GO annotation file.
Parameters
----------
path: str
The path name of the GO annotation file.
Returns
-------
str
The URL of the associated gene ontology file.
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thunder-project/thunder-registration | registration/transforms.py | Displacement.apply | def apply(self, im):
"""
Apply an n-dimensional displacement by shifting an image or volume.
Parameters
----------
im : ndarray
The image or volume to shift
"""
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"""
Apply an n-dimensional displacement by shifting an image or volume.
Parameters
----------
im : ndarray
The image or volume to shift
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thunder-project/thunder-registration | registration/transforms.py | Displacement.compute | def compute(a, b):
"""
Compute an optimal displacement between two ndarrays.
Finds the displacement between two ndimensional arrays. Arrays must be
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Compute an optimal displacement between two ndarrays.
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thunder-project/thunder-registration | registration/transforms.py | LocalDisplacement.compute | def compute(a, b, axis):
"""
Finds optimal displacements localized along an axis
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delta = []
for aa, bb in zip(rollaxis(a, axis, 0), rollaxis(b, axis, 0)):
delta.append(Displacement.compute(aa, bb).delta)
return LocalDisplacement(delta, axis=axis) | python | def compute(a, b, axis):
"""
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delta = []
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im : ndarray
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im : ndarray
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flo-compbio/genometools | genometools/ncbi/geo/functions.py | write_sample_sheet | def write_sample_sheet(output_file, accessions, names, celfile_urls, sel=None):
"""Generate a sample sheet in tab-separated text format.
The columns contain the following sample attributes:
1) accession
2) name
3) CEL file name
4) CEL file URL
Parameters
----------
output_file: str... | python | def write_sample_sheet(output_file, accessions, names, celfile_urls, sel=None):
"""Generate a sample sheet in tab-separated text format.
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@param command: Either a C{str} command (which will be passed to the
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@r... | python | def execute(self, command):
"""
Execute (or simulate) a command. Add to our log.
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acorg/dark-matter | dark/html.py | NCBISequenceLinkURL | def NCBISequenceLinkURL(title, default=None):
"""
Given a sequence title, like "gi|42768646|gb|AY516849.1| Homo sapiens",
return the URL of a link to the info page at NCBI.
title: the sequence title to produce a link URL for.
default: the value to return if the title cannot be parsed.
"""
t... | python | def NCBISequenceLinkURL(title, default=None):
"""
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title: the sequence title to produce a link URL for.
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acorg/dark-matter | dark/html.py | _sortHTML | def _sortHTML(titlesAlignments, by, limit=None):
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@param titlesAlignments: A L{dark.titles.TitlesAlignments} instance.
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"""
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acorg/dark-matter | dark/html.py | AlignmentPanelHTMLWriter._writeFASTA | def _writeFASTA(self, i, image):
"""
Write a FASTA file containing the set of reads that hit a sequence.
@param i: The number of the image in self._images.
@param image: A member of self._images.
@return: A C{str}, either 'fasta' or 'fastq' indicating the format
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"""
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acorg/dark-matter | dark/html.py | AlignmentPanelHTMLWriter._writeFeatures | def _writeFeatures(self, i, image):
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kyegupov/py-unrar2 | UnRAR2/windows.py | DosDateTimeToTimeTuple | def DosDateTimeToTimeTuple(dosDateTime):
"""Convert an MS-DOS format date time to a Python time tuple.
"""
dos_date = dosDateTime >> 16
dos_time = dosDateTime & 0xffff
day = dos_date & 0x1f
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year = 1980 + (dos_date >> 9)
second = 2 * (dos_time & 0x1f)
min... | python | def DosDateTimeToTimeTuple(dosDateTime):
"""Convert an MS-DOS format date time to a Python time tuple.
"""
dos_date = dosDateTime >> 16
dos_time = dosDateTime & 0xffff
day = dos_date & 0x1f
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second = 2 * (dos_time & 0x1f)
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acorg/dark-matter | dark/blast/score.py | bitScoreToEValue | def bitScoreToEValue(bitScore, dbSize, dbSequenceCount, queryLength,
lengthAdjustment):
"""
Convert a bit score to an e-value.
@param bitScore: The C{float} bit score to convert.
@param dbSize: The C{int} total size of the database (i.e., the sum of
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acorg/dark-matter | dark/blast/score.py | eValueToBitScore | def eValueToBitScore(eValue, dbSize, dbSequenceCount, queryLength,
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Convert an e-value to a bit score.
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acorg/dark-matter | dark/btop.py | parseBtop | def parseBtop(btopString):
"""
Parse a BTOP string.
The format is described at https://www.ncbi.nlm.nih.gov/books/NBK279682/
@param btopString: A C{str} BTOP sequence.
@raise ValueError: If C{btopString} is not valid BTOP.
@return: A generator that yields a series of integers and 2-tuples of
... | python | def parseBtop(btopString):
"""
Parse a BTOP string.
The format is described at https://www.ncbi.nlm.nih.gov/books/NBK279682/
@param btopString: A C{str} BTOP sequence.
@raise ValueError: If C{btopString} is not valid BTOP.
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acorg/dark-matter | dark/btop.py | countGaps | def countGaps(btopString):
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@param concise: If C{True}, use 'M' for matches and mismatches instead
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"""
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Peter-Slump/django-dynamic-fixtures | src/dynamic_fixtures/management/commands/load_dynamic_fixtures.py | Command.progress_callback | def progress_callback(self, action, node, elapsed_time=None):
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Callback to report progress
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:param list node: app, module
:param int | None elapsed_time:
"""
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flo-compbio/genometools | genometools/ontology/term.py | GOTerm.get_pretty_format | def get_pretty_format(self, include_id=True, max_name_length=0,
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flo-compbio/genometools | genometools/expression/normalize.py | quantile_normalize | def quantile_normalize(matrix, inplace=False, target=None):
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acorg/dark-matter | dark/hsp.py | HSP.toDict | def toDict(self):
"""
Get information about the HSP as a dictionary.
@return: A C{dict} representation of the HSP.
"""
result = _Base.toDict(self)
result['score'] = self.score.score
return result | python | def toDict(self):
"""
Get information about the HSP as a dictionary.
@return: A C{dict} representation of the HSP.
"""
result = _Base.toDict(self)
result['score'] = self.score.score
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flo-compbio/genometools | genometools/ensembl/filter_fasta.py | main | def main(args=None):
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args = parser.parse_args()
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"""Script body."""
if args is None:
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openfisca/openfisca-web-api | openfisca_web_api/application.py | make_app | def make_app(global_conf, **app_conf):
"""Create a WSGI application and return it
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nkavaldj/myhdl_lib | myhdl_lib/fifo_speculative.py | fifo_speculative | def fifo_speculative(rst, clk, full, we, din, empty, re, dout, wr_commit=None, wr_discard=None, rd_commit=None, rd_discard=None, afull=None, aempty=None, count=None, afull_th=None, aempty_th=None, ovf=None, udf=None, count_max=None, depth=None, width=None):
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acorg/dark-matter | dark/dimension.py | dimensionalIterator | def dimensionalIterator(dimensions, maxItems=-1):
"""
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n-tuples of coordinates to 'fill' the dimensions. This is like an
odometer in a car, but the dimensions do not each have to be 10.
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"""
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acorg/dark-matter | dark/dna.py | matchToString | def matchToString(dnaMatch, read1, read2, matchAmbiguous=True, indent='',
offsets=None):
"""
Format a DNA match as a string.
@param dnaMatch: A C{dict} returned by C{compareDNAReads}.
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Format a DNA match as a string.
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acorg/dark-matter | dark/dna.py | compareDNAReads | def compareDNAReads(read1, read2, matchAmbiguous=True, gapChars='-',
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Compare two DNA sequences.
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Compare two DNA sequences.
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acorg/dark-matter | dark/dna.py | findKozakConsensus | def findKozakConsensus(read):
"""
In a given DNA sequence, search for a Kozak consensus: (gcc)gccRccATGG.
The upper case bases in that pattern are required, and the lower case
bases are the ones most frequently found at the given positions. The
initial 'gcc' sequence (in parentheses) is of uncertain... | python | def findKozakConsensus(read):
"""
In a given DNA sequence, search for a Kozak consensus: (gcc)gccRccATGG.
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acorg/dark-matter | bin/check-fasta-json-blast-consistency.py | check | def check(fastaFile, jsonFiles):
"""
Check for simple consistency between the FASTA file and the JSON files.
Note that some checking is already performed by the BlastReadsAlignments
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BLAST records and that read ids and BLAST rec... | python | def check(fastaFile, jsonFiles):
"""
Check for simple consistency between the FASTA file and the JSON files.
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acorg/dark-matter | bin/fasta-identity-table.py | thresholdForIdentity | def thresholdForIdentity(identity, colors):
"""
Get the best identity threshold for a specific identity value.
@param identity: A C{float} nucleotide identity.
@param colors: A C{list} of (threshold, color) tuples, where threshold is a
C{float} and color is a C{str} to be used as a cell backgro... | python | def thresholdForIdentity(identity, colors):
"""
Get the best identity threshold for a specific identity value.
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acorg/dark-matter | bin/fasta-identity-table.py | parseColors | def parseColors(colors, defaultColor):
"""
Parse command line color information.
@param colors: A C{list} of space separated "value color" strings, such as
["0.9 red", "0.75 rgb(23, 190, 207)", "0.1 #CF3CF3"].
@param defaultColor: The C{str} color to use for cells that do not reach
the ... | python | def parseColors(colors, defaultColor):
"""
Parse command line color information.
@param colors: A C{list} of space separated "value color" strings, such as
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acorg/dark-matter | bin/fasta-identity-table.py | getReadLengths | def getReadLengths(reads, gapChars):
"""
Get all read lengths, excluding gap characters.
@param reads: A C{Reads} instance.
@param gapChars: A C{str} of sequence characters considered to be gaps.
@return: A C{dict} keyed by read id, with C{int} length values.
"""
gapChars = set(gapChars)
... | python | def getReadLengths(reads, gapChars):
"""
Get all read lengths, excluding gap characters.
@param reads: A C{Reads} instance.
@param gapChars: A C{str} of sequence characters considered to be gaps.
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acorg/dark-matter | bin/fasta-identity-table.py | explanation | def explanation(matchAmbiguous, concise, showLengths, showGaps, showNs):
"""
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acorg/dark-matter | bin/fasta-identity-table.py | collectData | def collectData(reads1, reads2, square, matchAmbiguous):
"""
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@param reads1: An C{OrderedDict} of C{str} read ids whose values are
C{Read} instances. These will be the rows of the table.
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acorg/dark-matter | bin/fasta-identity-table.py | simpleTable | def simpleTable(tableData, reads1, reads2, square, matchAmbiguous, gapChars):
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@param tableData: A C{defaultdict(dict)} keyed by read ids, whose values
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Make a text table showing inter-sequence distances.
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acorg/dark-matter | bin/fasta-identity-table.py | htmlTable | def htmlTable(tableData, reads1, reads2, square, matchAmbiguous, colors,
concise=False, showLengths=False, showGaps=False, showNs=False,
footer=False, div=False, gapChars='-'):
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invenia/Arbiter | arbiter/task.py | create_task | def create_task(function, *args, **kwargs):
"""
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function: The actual task function. It should take no arguments,
and return a False-y value if it fails.
dependencies: (optional, ()) Any dependencies that this task relies
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"""
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"""
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function: The actual task function. It should take no arguments,
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nkavaldj/myhdl_lib | myhdl_lib/handshake.py | hs_join | def hs_join(ls_hsi, hso):
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ls_hsi - (i) list of input handshake tuples (ready, valid)
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nkavaldj/myhdl_lib | myhdl_lib/handshake.py | hs_fork | def hs_fork(hsi, ls_hso):
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hsi - (i) input handshake tuple (ready, valid)
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nkavaldj/myhdl_lib | myhdl_lib/handshake.py | hs_mux | def hs_mux(sel, ls_hsi, hso):
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nkavaldj/myhdl_lib | myhdl_lib/handshake.py | hs_demux | def hs_demux(sel, hsi, ls_hso):
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nkavaldj/myhdl_lib | myhdl_lib/handshake.py | hs_arbmux | def hs_arbmux(rst, clk, ls_hsi, hso, sel, ARBITER_TYPE="priority"):
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Selects one of the active input interfaces and connects it to the output.
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nkavaldj/myhdl_lib | myhdl_lib/handshake.py | hs_arbdemux | def hs_arbdemux(rst, clk, hsi, ls_hso, sel, ARBITER_TYPE="priority"):
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flo-compbio/genometools | genometools/misc/functions.py | get_file_md5sum | def get_file_md5sum(path):
"""Calculate the MD5 hash for a file."""
with open(path, 'rb') as fh:
h = str(hashlib.md5(fh.read()).hexdigest())
return h | python | def get_file_md5sum(path):
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flo-compbio/genometools | genometools/misc/functions.py | smart_open_read | def smart_open_read(path=None, mode='rb', encoding=None, try_gzip=False):
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flo-compbio/genometools | genometools/misc/functions.py | smart_open_write | def smart_open_write(path=None, mode='wb', encoding=None):
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Adapted from StackOverflow user "Wolph"
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"""
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flo-compbio/genometools | genometools/misc/functions.py | get_url_size | def get_url_size(url):
"""Get the size of a URL.
Note: Uses requests, so it does not work for FTP URLs.
Source: StackOverflow user "Burhan Khalid".
(http://stackoverflow.com/a/24585314/5651021)
Parameters
----------
url : str
The URL.
Returns
-------
int
The s... | python | def get_url_size(url):
"""Get the size of a URL.
Note: Uses requests, so it does not work for FTP URLs.
Source: StackOverflow user "Burhan Khalid".
(http://stackoverflow.com/a/24585314/5651021)
Parameters
----------
url : str
The URL.
Returns
-------
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flo-compbio/genometools | genometools/misc/functions.py | get_url_file_name | def get_url_file_name(url):
"""Get the file name from an url
Parameters
----------
url : str
Returns
-------
str
The file name
"""
assert isinstance(url, (str, _oldstr))
return urlparse.urlparse(url).path.split('/')[-1] | python | def get_url_file_name(url):
"""Get the file name from an url
Parameters
----------
url : str
Returns
-------
str
The file name
"""
assert isinstance(url, (str, _oldstr))
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flo-compbio/genometools | genometools/misc/functions.py | make_sure_dir_exists | def make_sure_dir_exists(dir_, create_subfolders=False):
"""Ensures that a directory exists.
Adapted from StackOverflow users "Bengt" and "Heikki Toivonen"
(http://stackoverflow.com/a/5032238).
Parameters
----------
dir_: str
The directory path.
create_subfolders: bool, optional
... | python | def make_sure_dir_exists(dir_, create_subfolders=False):
"""Ensures that a directory exists.
Adapted from StackOverflow users "Bengt" and "Heikki Toivonen"
(http://stackoverflow.com/a/5032238).
Parameters
----------
dir_: str
The directory path.
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flo-compbio/genometools | genometools/misc/functions.py | get_file_size | def get_file_size(path):
"""The the size of a file in bytes.
Parameters
----------
path: str
The path of the file.
Returns
-------
int
The size of the file in bytes.
Raises
------
IOError
If the file does not exist.
OSError
If a file system ... | python | def get_file_size(path):
"""The the size of a file in bytes.
Parameters
----------
path: str
The path of the file.
Returns
-------
int
The size of the file in bytes.
Raises
------
IOError
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OSError
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flo-compbio/genometools | genometools/misc/functions.py | get_file_checksum | def get_file_checksum(path):
"""Get the checksum of a file (using ``sum``, Unix-only).
This function is only available on certain platforms.
Parameters
----------
path: str
The path of the file.
Returns
-------
int
The checksum.
Raises
------
IOError
... | python | def get_file_checksum(path):
"""Get the checksum of a file (using ``sum``, Unix-only).
This function is only available on certain platforms.
Parameters
----------
path: str
The path of the file.
Returns
-------
int
The checksum.
Raises
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IOError
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flo-compbio/genometools | genometools/misc/functions.py | gzip_open_text | def gzip_open_text(path, encoding=None):
"""Opens a plain-text file that may be gzip'ed.
Parameters
----------
path : str
The file.
encoding : str, optional
The encoding to use.
Returns
-------
file-like
A file-like object.
Notes
-----
Generally, re... | python | def gzip_open_text(path, encoding=None):
"""Opens a plain-text file that may be gzip'ed.
Parameters
----------
path : str
The file.
encoding : str, optional
The encoding to use.
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flo-compbio/genometools | genometools/misc/functions.py | bisect_index | def bisect_index(a, x):
""" Find the leftmost index of an element in a list using binary search.
Parameters
----------
a: list
A sorted list.
x: arbitrary
The element.
Returns
-------
int
The index.
"""
i = bisect.bisect_left(a, x)
if i != len(a) an... | python | def bisect_index(a, x):
""" Find the leftmost index of an element in a list using binary search.
Parameters
----------
a: list
A sorted list.
x: arbitrary
The element.
Returns
-------
int
The index.
"""
i = bisect.bisect_left(a, x)
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flo-compbio/genometools | genometools/misc/functions.py | read_single | def read_single(path, encoding = 'UTF-8'):
""" Reads the first column of a tab-delimited text file.
The file can either be uncompressed or gzip'ed.
Parameters
----------
path: str
The path of the file.
enc: str
The file encoding.
Returns
-------
List of str
... | python | def read_single(path, encoding = 'UTF-8'):
""" Reads the first column of a tab-delimited text file.
The file can either be uncompressed or gzip'ed.
Parameters
----------
path: str
The path of the file.
enc: str
The file encoding.
Returns
-------
List of str
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flo-compbio/genometools | genometools/gcloud/compute/network.py | add_tcp_firewall_rule | def add_tcp_firewall_rule(project, access_token, name, tag, port):
"""Adds a TCP firewall rule.
TODO: docstring"""
headers = {
'Authorization': 'Bearer %s' % access_token.access_token
}
payload = {
"name": name,
"kind": "compute#firewall",
"sourceRanges": [... | python | def add_tcp_firewall_rule(project, access_token, name, tag, port):
"""Adds a TCP firewall rule.
TODO: docstring"""
headers = {
'Authorization': 'Bearer %s' % access_token.access_token
}
payload = {
"name": name,
"kind": "compute#firewall",
"sourceRanges": [... | [
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cebel/pyuniprot | src/pyuniprot/cli.py | update | def update(taxids, conn, force_download, silent):
"""Update local UniProt database"""
if not silent:
click.secho("WARNING: Update is very time consuming and can take several "
"hours depending which organisms you are importing!", fg="yellow")
if not taxids:
click... | python | def update(taxids, conn, force_download, silent):
"""Update local UniProt database"""
if not silent:
click.secho("WARNING: Update is very time consuming and can take several "
"hours depending which organisms you are importing!", fg="yellow")
if not taxids:
click... | [
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cebel/pyuniprot | src/pyuniprot/cli.py | web | def web(host, port):
"""Start web application"""
from .webserver.web import get_app
get_app().run(host=host, port=port) | python | def web(host, port):
"""Start web application"""
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cebel/pyuniprot | src/pyuniprot/cli.py | connection | def connection(connection, without_connection_test):
"""Set MySQL/MariaDB connection"""
database.set_connection(connection=connection)
if not without_connection_test:
test_connection(connection) | python | def connection(connection, without_connection_test):
"""Set MySQL/MariaDB connection"""
database.set_connection(connection=connection)
if not without_connection_test:
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acorg/dark-matter | dark/blast/params.py | checkCompatibleParams | def checkCompatibleParams(initialParams, laterParams):
"""
Check a later set of BLAST parameters against those originally found.
@param initialParams: A C{dict} with the originally encountered BLAST
parameter settings.
@param laterParams: A C{dict} with BLAST parameter settings encountered
... | python | def checkCompatibleParams(initialParams, laterParams):
"""
Check a later set of BLAST parameters against those originally found.
@param initialParams: A C{dict} with the originally encountered BLAST
parameter settings.
@param laterParams: A C{dict} with BLAST parameter settings encountered
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flo-compbio/genometools | genometools/basic/gene_set.py | GeneSet.to_list | def to_list(self):
"""Converts the GeneSet object to a flat list of strings.
Note: see also :meth:`from_list`.
Parameters
----------
Returns
-------
list of str
The data from the GeneSet object as a flat list.
"""
src = self._source ... | python | def to_list(self):
"""Converts the GeneSet object to a flat list of strings.
Note: see also :meth:`from_list`.
Parameters
----------
Returns
-------
list of str
The data from the GeneSet object as a flat list.
"""
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