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bxlab/bx-python | lib/bx_extras/pyparsing.py | countedArray | def countedArray( expr ):
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bxlab/bx-python | lib/bx_extras/pyparsing.py | nestedExpr | def nestedExpr(opener="(", closer=")", content=None, ignoreExpr=quotedString):
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bxlab/bx-python | lib/bx_extras/pyparsing.py | ParserElement.setBreak | def setBreak(self,breakFlag = True):
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"""Method to invoke the Python pdb debugger when this element is
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bxlab/bx-python | lib/bx_extras/pyparsing.py | ParserElement._normalizeParseActionArgs | def _normalizeParseActionArgs( f ):
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bxlab/bx-python | lib/bx_extras/pyparsing.py | ParserElement.parseString | def parseString( self, instring, parseAll=False ):
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bxlab/bx-python | lib/bx_extras/pyparsing.py | ParserElement.transformString | def transformString( self, instring ):
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bxlab/bx-python | lib/bx_extras/pyparsing.py | ParserElement.searchString | def searchString( self, instring, maxMatches=_MAX_INT ):
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bxlab/bx-python | lib/bx_extras/pyparsing.py | ParserElement.parseFile | def parseFile( self, file_or_filename ):
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bxlab/bx-python | lib/bx/align/epo.py | Chain._strfactory | def _strfactory(cls, line):
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:param line: header of a chain (in .chain format)
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assert type(line) == str, "this is a factory from string"
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bxlab/bx-python | lib/bx/align/epo.py | Chain._make_from_epo | def _make_from_epo(cls, trg_comp, qr_comp, trg_chrom_sizes, qr_chrom_sizes):
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bxlab/bx-python | lib/bx/align/epo.py | Chain._parse_file | def _parse_file(cls, path, pickle=False):
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fname = path
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#you asked for... | python | def _parse_file(cls, path, pickle=False):
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bxlab/bx-python | lib/bx/align/epo.py | EPOitem._strfactory | def _strfactory(cls, line):
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bxlab/bx-python | lib/bx/align/epo.py | EPOitem._parse_epo | def _parse_epo(cls, fname):
"""Load an entire file in the EPO format into a dictionary of the type {gab_id => [Epoitem, ...]}
:param fname: file name"""
data = {}
with open(fname) as fd:
for el in (cls._strfactory(_) for _ in fd):
if el:
... | python | def _parse_epo(cls, fname):
"""Load an entire file in the EPO format into a dictionary of the type {gab_id => [Epoitem, ...]}
:param fname: file name"""
data = {}
with open(fname) as fd:
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bxlab/bx-python | lib/bx/align/epo.py | EPOitem.cigar_iter | def cigar_iter(self, reverse):
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bxlab/bx-python | lib/bx/align/epo.py | EPOitem.intervals | def intervals(self, reverse, thr=0):
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"""return a list of (0-based half-open) intervals representing the match regions of the cigar
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bxlab/bx-python | scripts/maf_tile_2.py | do_interval | def do_interval( sources, index, out, ref_src, start, end, seq_db, missing_data, strand ):
"""
Join together alignment blocks to create a semi human projected local
alignment (small reference sequence deletions are kept as supported by
the local alignment).
"""
ref_src_size = None
# Make s... | python | def do_interval( sources, index, out, ref_src, start, end, seq_db, missing_data, strand ):
"""
Join together alignment blocks to create a semi human projected local
alignment (small reference sequence deletions are kept as supported by
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bxlab/bx-python | lib/bx/bitset_builders.py | binned_bitsets_from_file | def binned_bitsets_from_file( f, chrom_col=0, start_col=1, end_col=2, strand_col=5, upstream_pad=0, downstream_pad=0, lens={} ):
"""
Read a file into a dictionary of bitsets. The defaults arguments
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- 'chrom_col', 'start_col', ... | python | def binned_bitsets_from_file( f, chrom_col=0, start_col=1, end_col=2, strand_col=5, upstream_pad=0, downstream_pad=0, lens={} ):
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bxlab/bx-python | lib/bx/bitset_builders.py | binned_bitsets_proximity | def binned_bitsets_proximity( f, chrom_col=0, start_col=1, end_col=2, strand_col=5, upstream=0, downstream=0 ):
"""Read a file into a dictionary of bitsets"""
last_chrom = None
last_bitset = None
bitsets = dict()
for line in f:
if line.startswith("#"): continue
# print "input=%s" % ( ... | python | def binned_bitsets_proximity( f, chrom_col=0, start_col=1, end_col=2, strand_col=5, upstream=0, downstream=0 ):
"""Read a file into a dictionary of bitsets"""
last_chrom = None
last_bitset = None
bitsets = dict()
for line in f:
if line.startswith("#"): continue
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bxlab/bx-python | lib/bx/bitset_builders.py | binned_bitsets_from_list | def binned_bitsets_from_list( list=[] ):
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bxlab/bx-python | lib/bx/bitset_builders.py | binned_bitsets_by_chrom | def binned_bitsets_by_chrom( f, chrom, chrom_col=0, start_col=1, end_col=2):
"""Read a file by chrom name into a bitset"""
bitset = BinnedBitSet( MAX )
for line in f:
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fields = line.split()
if fields[chrom_col] == chrom:
start, end = int( ... | python | def binned_bitsets_by_chrom( f, chrom, chrom_col=0, start_col=1, end_col=2):
"""Read a file by chrom name into a bitset"""
bitset = BinnedBitSet( MAX )
for line in f:
if line.startswith("#"): continue
fields = line.split()
if fields[chrom_col] == chrom:
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bxlab/bx-python | lib/bx/align/tools/chop.py | chop_list | def chop_list( blocks, src, start, end ):
"""
For each alignment block in the sequence `blocks`, chop out the portion
of the block that overlaps the interval [`start`,`end`) in the
component/species named `src`.
"""
new_blocks = []
for block in blocks:
ref = block.get_component_by_s... | python | def chop_list( blocks, src, start, end ):
"""
For each alignment block in the sequence `blocks`, chop out the portion
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new_blocks = []
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bxlab/bx-python | lib/bx_extras/fpconst.py | _double_as_bytes | def _double_as_bytes(dval):
"Use struct.unpack to decode a double precision float into eight bytes"
tmp = list(struct.unpack('8B',struct.pack('d', dval)))
if not _big_endian:
tmp.reverse()
return tmp | python | def _double_as_bytes(dval):
"Use struct.unpack to decode a double precision float into eight bytes"
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bxlab/bx-python | lib/bx_extras/fpconst.py | _mantissa | def _mantissa(dval):
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mantissa = bb[1] & 0x0f << 48
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mantissa += bb[3] << 32
mantissa += bb[4]
return mantissa | python | def _mantissa(dval):
"""Extract the _mantissa bits from a double-precision floating
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bb = _double_as_bytes(dval)
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mantissa += bb[2] << 40
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bxlab/bx-python | lib/bx_extras/fpconst.py | _zero_mantissa | def _zero_mantissa(dval):
"""Determine whether the mantissa bits of the given double are all
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bb = _double_as_bytes(dval)
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"""Determine whether the mantissa bits of the given double are all
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bxlab/bx-python | scripts/aggregate_scores_in_intervals.py | load_scores_wiggle | def load_scores_wiggle( fname ):
"""
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"""
scores_by_chrom = dict()
for chrom, pos, val in bx.wiggle.Reader( misc.open_compressed( fname ) ):
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scores_by_chrom[chrom... | python | def load_scores_wiggle( fname ):
"""
Read a wiggle file and return a dict of BinnedArray objects keyed
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"""
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bxlab/bx-python | lib/bx/interval_index_file.py | offsets_for_max_size | def offsets_for_max_size( max_size ):
"""
Return the subset of offsets needed to contain intervals over (0,max_size)
"""
for i, max in enumerate( reversed( BIN_OFFSETS_MAX ) ):
if max_size < max:
break
else:
raise Exception( "%d is larger than the maximum possible size (%... | python | def offsets_for_max_size( max_size ):
"""
Return the subset of offsets needed to contain intervals over (0,max_size)
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bxlab/bx-python | lib/bx/interval_index_file.py | bin_for_range | def bin_for_range( start, end, offsets=None ):
"""Find the smallest bin that can contain interval (start,end)"""
if offsets is None:
offsets = BIN_OFFSETS
start_bin, end_bin = start, max(start, end - 1)
start_bin >>= BIN_FIRST_SHIFT
end_bin >>= BIN_FIRST_SHIFT
for offset in offsets:
... | python | def bin_for_range( start, end, offsets=None ):
"""Find the smallest bin that can contain interval (start,end)"""
if offsets is None:
offsets = BIN_OFFSETS
start_bin, end_bin = start, max(start, end - 1)
start_bin >>= BIN_FIRST_SHIFT
end_bin >>= BIN_FIRST_SHIFT
for offset in offsets:
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bxlab/bx-python | lib/bx/interval_index_file.py | Index.new | def new( self, min, max ):
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# Determine offsets to use
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bxlab/bx-python | lib/bx/interval_index_file.py | Index.add | def add( self, start, end, val ):
"""Add the interval (start,end) with associated value val to the index"""
insort( self.bins[ bin_for_range( start, end, offsets=self.offsets ) ], ( start, end, val ) )
assert val >= 0
self.max_val = max(self.max_val,val) | python | def add( self, start, end, val ):
"""Add the interval (start,end) with associated value val to the index"""
insort( self.bins[ bin_for_range( start, end, offsets=self.offsets ) ], ( start, end, val ) )
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bxlab/bx-python | lib/bx/misc/filecache.py | FileCache.seek | def seek( self, offset, whence=0 ):
"""
Move the file pointer to a particular offset.
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# Determine absolute target position
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target_pos = offset
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target_pos = self.file_pos + offset
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"""
Move the file pointer to a particular offset.
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# Determine absolute target position
if whence == 0:
target_pos = offset
elif whence == 1:
target_pos = self.file_pos + offset
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bxlab/bx-python | lib/bx_extras/lrucache.py | LRUCache.mtime | def mtime(self, key):
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if key not in self.__dict:
raise CacheKeyError(key)
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bxlab/bx-python | lib/bx/cookbook/attribute.py | class_space | def class_space(classlevel=3):
"returns the calling class' name and dictionary"
frame = sys._getframe(classlevel)
classname = frame.f_code.co_name
classdict = frame.f_locals
return classname, classdict | python | def class_space(classlevel=3):
"returns the calling class' name and dictionary"
frame = sys._getframe(classlevel)
classname = frame.f_code.co_name
classdict = frame.f_locals
return classname, classdict | [
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bxlab/bx-python | lib/bx/cookbook/attribute.py | _attribute | def _attribute(permission='rwd', **kwds):
"""returns one property for each (key,value) pair in kwds;
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'r': readable, 'w':writable, 'd':deletable
"""
classname, classdict = class_space()
def _property(attrname, default):
... | python | def _attribute(permission='rwd', **kwds):
"""returns one property for each (key,value) pair in kwds;
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'r': readable, 'w':writable, 'd':deletable
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classname, classdict = class_space()
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bxlab/bx-python | lib/bx/align/lav.py | Reader.parse_a_stanza | def parse_a_stanza(self):
"""returns the pair (score,pieces)
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with start1,start2 origin-0"""
# 's' line -- score, 1 field
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assert (fields[0] == "s"), "s line exp... | python | def parse_a_stanza(self):
"""returns the pair (score,pieces)
where pieces is a list of ungapped segments (start1,start2,length,pctId)
with start1,start2 origin-0"""
# 's' line -- score, 1 field
line = self.fetch_line(report=" in a-stanza")
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bxlab/bx-python | lib/bx/align/lav.py | Reader.build_alignment | def build_alignment(self,score,pieces):
"""converts a score and pieces to an alignment"""
# build text
self.open_seqs()
text1 = text2 = ""
end1 = end2 = None
for (start1,start2,length,pctId) in pieces:
if (end1 != None):
if (start1 == end1): # insertion in sequence 2
text1 += self.seq1_gap * ... | python | def build_alignment(self,score,pieces):
"""converts a score and pieces to an alignment"""
# build text
self.open_seqs()
text1 = text2 = ""
end1 = end2 = None
for (start1,start2,length,pctId) in pieces:
if (end1 != None):
if (start1 == end1): # insertion in sequence 2
text1 += self.seq1_gap * ... | [
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bxlab/bx-python | lib/bx/intervals/operations/__init__.py | bits_clear_in_range | def bits_clear_in_range( bits, range_start, range_end ):
"""
Yield start,end tuples for each span of clear bits in [range_start,range_end)
"""
end = range_start
while 1:
start = bits.next_clear( end )
if start >= range_end: break
end = min( bits.next_set( start ), range_end )... | python | def bits_clear_in_range( bits, range_start, range_end ):
"""
Yield start,end tuples for each span of clear bits in [range_start,range_end)
"""
end = range_start
while 1:
start = bits.next_clear( end )
if start >= range_end: break
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bxlab/bx-python | lib/bx/cookbook/progress_bar.py | iterprogress | def iterprogress( sized_iterable ):
"""
Iterate something printing progress bar to stdout
"""
pb = ProgressBar( 0, len( sized_iterable ) )
for i, value in enumerate( sized_iterable ):
yield value
pb.update_and_print( i, sys.stderr ) | python | def iterprogress( sized_iterable ):
"""
Iterate something printing progress bar to stdout
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pb = ProgressBar( 0, len( sized_iterable ) )
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bxlab/bx-python | lib/bx/misc/cdb.py | FileCDBDict.to_file | def to_file( Class, dict, file, is_little_endian=True ):
"""
For constructing a CDB structure in a file. Able to calculate size on
disk and write to a file
"""
io = BinaryFileWriter( file, is_little_endian=is_little_endian )
start_offset = io.tell()
# Header is of... | python | def to_file( Class, dict, file, is_little_endian=True ):
"""
For constructing a CDB structure in a file. Able to calculate size on
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"""
io = BinaryFileWriter( file, is_little_endian=is_little_endian )
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bxlab/bx-python | scripts/bed_complement.py | read_len | def read_len( f ):
"""Read a 'LEN' file and return a mapping from chromosome to length"""
mapping = dict()
for line in f:
fields = line.split()
mapping[ fields[0] ] = int( fields[1] )
return mapping | python | def read_len( f ):
"""Read a 'LEN' file and return a mapping from chromosome to length"""
mapping = dict()
for line in f:
fields = line.split()
mapping[ fields[0] ] = int( fields[1] )
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bxlab/bx-python | lib/bx/motif/logo/__init__.py | freqs_to_heights | def freqs_to_heights( matrix ):
"""
Calculate logo height using the method of:
Schneider TD, Stephens RM. "Sequence logos: a new way to display consensus
sequences." Nucleic Acids Res. 1990 Oct 25;18(20):6097-100.
"""
# Columns are sequence positions, rows are symbol counts/frequencies
... | python | def freqs_to_heights( matrix ):
"""
Calculate logo height using the method of:
Schneider TD, Stephens RM. "Sequence logos: a new way to display consensus
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"""
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bxlab/bx-python | lib/bx/motif/logo/__init__.py | eps_logo | def eps_logo( matrix, base_width, height, colors=DNA_DEFAULT_COLORS ):
"""
Return an EPS document containing a sequence logo for matrix where each
bases is shown as a column of `base_width` points and the total logo
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characters t... | python | def eps_logo( matrix, base_width, height, colors=DNA_DEFAULT_COLORS ):
"""
Return an EPS document containing a sequence logo for matrix where each
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bxlab/bx-python | scripts/bnMapper.py | transform | def transform(elem, chain_CT_CQ, max_gap):
"""transform the coordinates of this elem into the other species.
elem intersects this chain's ginterval.
:return: a list of the type [(to_chr, start, end, elem[id]) ... ]"""
(chain, CT, CQ) = chain_CT_CQ
start, end = max(elem['start'], chain.tStart) - cha... | python | def transform(elem, chain_CT_CQ, max_gap):
"""transform the coordinates of this elem into the other species.
elem intersects this chain's ginterval.
:return: a list of the type [(to_chr, start, end, elem[id]) ... ]"""
(chain, CT, CQ) = chain_CT_CQ
start, end = max(elem['start'], chain.tStart) - cha... | [
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bxlab/bx-python | scripts/bnMapper.py | union_elements | def union_elements(elements):
"""elements = [(chr, s, e, id), ...], this is to join elements that have a
deletion in the 'to' species
"""
if len(elements) < 2: return elements
assert set( [e[3] for e in elements] ) == set( [elements[0][3]] ), "more than one id"
el_id = elements[0][3]
union... | python | def union_elements(elements):
"""elements = [(chr, s, e, id), ...], this is to join elements that have a
deletion in the 'to' species
"""
if len(elements) < 2: return elements
assert set( [e[3] for e in elements] ) == set( [elements[0][3]] ), "more than one id"
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bxlab/bx-python | scripts/bnMapper.py | transform_file | def transform_file(ELEMS, ofname, EPO, TREE, opt):
"transform/map the elements of this file and dump the output on 'ofname'"
BED4_FRM = "%s\t%d\t%d\t%s\n"
log.info("%s (%d) elements ..." % (opt.screen and "screening" or "transforming", ELEMS.shape[0]))
with open(ofname, 'w') as out_fd:
if opt.s... | python | def transform_file(ELEMS, ofname, EPO, TREE, opt):
"transform/map the elements of this file and dump the output on 'ofname'"
BED4_FRM = "%s\t%d\t%d\t%s\n"
log.info("%s (%d) elements ..." % (opt.screen and "screening" or "transforming", ELEMS.shape[0]))
with open(ofname, 'w') as out_fd:
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bxlab/bx-python | scripts/bnMapper.py | loadChains | def loadChains(path):
"name says it."
EPO = epo.Chain._parse_file(path, True)
## convert coordinates w.r.t the forward strand (into slices)
## compute cummulative intervals
for i in range( len(EPO) ):
ch, S, T, Q = EPO[i]
if ch.tStrand == '-':
ch = ch._replace(tEnd = ch.... | python | def loadChains(path):
"name says it."
EPO = epo.Chain._parse_file(path, True)
## convert coordinates w.r.t the forward strand (into slices)
## compute cummulative intervals
for i in range( len(EPO) ):
ch, S, T, Q = EPO[i]
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bxlab/bx-python | scripts/bnMapper.py | loadFeatures | def loadFeatures(path, opt):
"""
Load features. For BED, only BED4 columns are loaded.
For narrowPeak, all columns are loaded.
"""
log.info("loading from %s ..." % path)
data = []
if opt.in_format == "BED":
with open(path) as fd:
for line in fd:
c... | python | def loadFeatures(path, opt):
"""
Load features. For BED, only BED4 columns are loaded.
For narrowPeak, all columns are loaded.
"""
log.info("loading from %s ..." % path)
data = []
if opt.in_format == "BED":
with open(path) as fd:
for line in fd:
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bxlab/bx-python | scripts/bnMapper.py | GIntervalTree.add | def add(self, chrom, element):
"""insert an element. use this method as the IntervalTree one.
this will simply call the IntervalTree.add method on the right tree
:param chrom: chromosome
:param element: the argument of IntervalTree.insert_interval
:return: None
"""
... | python | def add(self, chrom, element):
"""insert an element. use this method as the IntervalTree one.
this will simply call the IntervalTree.add method on the right tree
:param chrom: chromosome
:param element: the argument of IntervalTree.insert_interval
:return: None
"""
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bxlab/bx-python | scripts/bnMapper.py | GIntervalTree.find | def find(self, chrom, start, end):
"""find the intersecting elements
:param chrom: chromosome
:param start: start
:param end: end
:return: a list of intersecting elements"""
tree = self._trees.get( chrom, None )
if tree:
return tree.find( start, end ... | python | def find(self, chrom, start, end):
"""find the intersecting elements
:param chrom: chromosome
:param start: start
:param end: end
:return: a list of intersecting elements"""
tree = self._trees.get( chrom, None )
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bxlab/bx-python | lib/bx/motif/pwm.py | BaseMatrix.from_rows | def from_rows( Class, alphabet, rows ):
"""
Create a new matrix for a sequence over alphabet `alphabet` taking
values from `rows` which is a list whose length is the width of the
matrix, and whose elements are lists of values associated with each
character (in the order those ch... | python | def from_rows( Class, alphabet, rows ):
"""
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bxlab/bx-python | lib/bx/motif/pwm.py | BaseMatrix.create_from_other | def create_from_other( Class, other, values=None ):
"""
Create a new Matrix with attributes taken from `other` but with the
values taken from `values` if provided
"""
m = Class()
m.alphabet = other.alphabet
m.sorted_alphabet = other.sorted_alphabet
m.char... | python | def create_from_other( Class, other, values=None ):
"""
Create a new Matrix with attributes taken from `other` but with the
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"""
m = Class()
m.alphabet = other.alphabet
m.sorted_alphabet = other.sorted_alphabet
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bxlab/bx-python | lib/bx/motif/pwm.py | BaseMatrix.reverse_complement | def reverse_complement( self ):
"""
Create the reverse complement of this matrix. The result probably
only makese sense if the alphabet is that of DNA ('A','C','G','T').
"""
rval = copy( self )
# Conveniently enough, reversing rows and columns is exactly what we
#... | python | def reverse_complement( self ):
"""
Create the reverse complement of this matrix. The result probably
only makese sense if the alphabet is that of DNA ('A','C','G','T').
"""
rval = copy( self )
# Conveniently enough, reversing rows and columns is exactly what we
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bxlab/bx-python | lib/bx/motif/pwm.py | FrequencyMatrix.to_logodds_scoring_matrix | def to_logodds_scoring_matrix( self, background=None, correction=DEFAULT_CORRECTION ):
"""
Create a standard logodds scoring matrix.
"""
alphabet_size = len( self.alphabet )
if background is None:
background = ones( alphabet_size, float32 ) / alphabet_size
# R... | python | def to_logodds_scoring_matrix( self, background=None, correction=DEFAULT_CORRECTION ):
"""
Create a standard logodds scoring matrix.
"""
alphabet_size = len( self.alphabet )
if background is None:
background = ones( alphabet_size, float32 ) / alphabet_size
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bxlab/bx-python | lib/bx/motif/pwm.py | FrequencyMatrix.to_stormo_scoring_matrix | def to_stormo_scoring_matrix( self, background=None ):
"""
Create a scoring matrix from this count matrix using the method from:
Hertz, G.Z. and G.D. Stormo (1999). Identifying DNA and protein patterns with statistically
significant alignments of multiple sequences. Bioinformatics 15(7... | python | def to_stormo_scoring_matrix( self, background=None ):
"""
Create a scoring matrix from this count matrix using the method from:
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bxlab/bx-python | lib/bx/motif/pwm.py | ScoringMatrix.score_string | def score_string( self, string ):
"""
Score each valid position in `string` using this scoring matrix.
Positions which were not scored are set to nan.
"""
rval = zeros( len( string ), float32 )
rval[:] = nan
_pwm.score_string( self.values, self.char_to_index, str... | python | def score_string( self, string ):
"""
Score each valid position in `string` using this scoring matrix.
Positions which were not scored are set to nan.
"""
rval = zeros( len( string ), float32 )
rval[:] = nan
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jborean93/ntlm-auth | ntlm_auth/compute_keys.py | _get_exchange_key_ntlm_v1 | def _get_exchange_key_ntlm_v1(negotiate_flags, session_base_key,
server_challenge, lm_challenge_response,
lm_hash):
"""
[MS-NLMP] v28.0 2016-07-14
3.4.5.1 KXKEY
Calculates the Key Exchange Key for NTLMv1 authentication. Used for signing
an... | python | def _get_exchange_key_ntlm_v1(negotiate_flags, session_base_key,
server_challenge, lm_challenge_response,
lm_hash):
"""
[MS-NLMP] v28.0 2016-07-14
3.4.5.1 KXKEY
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jborean93/ntlm-auth | ntlm_auth/compute_keys.py | _get_seal_key_ntlm1 | def _get_seal_key_ntlm1(negotiate_flags, exported_session_key):
"""
3.4.5.3 SEALKEY
Calculates the seal_key used to seal (encrypt) messages. This for
authentication where NTLMSSP_NEGOTIATE_EXTENDED_SESSIONSECURITY has not
been negotiated. Will weaken the keys if NTLMSSP_NEGOTIATE_56 is not
negot... | python | def _get_seal_key_ntlm1(negotiate_flags, exported_session_key):
"""
3.4.5.3 SEALKEY
Calculates the seal_key used to seal (encrypt) messages. This for
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jborean93/ntlm-auth | ntlm_auth/compute_response.py | ComputeResponse.get_nt_challenge_response | def get_nt_challenge_response(self, lm_challenge_response,
server_certificate_hash=None, cbt_data=None):
"""
[MS-NLMP] v28.0 2016-07-14
3.3.1 - NTLM v1 Authentication
3.3.2 - NTLM v2 Authentication
This method returns the NtChallengeResponse ke... | python | def get_nt_challenge_response(self, lm_challenge_response,
server_certificate_hash=None, cbt_data=None):
"""
[MS-NLMP] v28.0 2016-07-14
3.3.1 - NTLM v1 Authentication
3.3.2 - NTLM v2 Authentication
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jborean93/ntlm-auth | ntlm_auth/compute_response.py | ComputeResponse._get_LMv2_response | def _get_LMv2_response(user_name, password, domain_name, server_challenge,
client_challenge):
"""
[MS-NLMP] v28.0 2016-07-14
2.2.2.4 LMv2_RESPONSE
The LMv2_RESPONSE structure defines the NTLM v2 authentication
LmChallengeResponse in the AUTHENTICATE_ME... | python | def _get_LMv2_response(user_name, password, domain_name, server_challenge,
client_challenge):
"""
[MS-NLMP] v28.0 2016-07-14
2.2.2.4 LMv2_RESPONSE
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jborean93/ntlm-auth | ntlm_auth/compute_response.py | ComputeResponse._get_NTLM2_response | def _get_NTLM2_response(password, server_challenge, client_challenge):
"""
[MS-NLMP] v28.0 2016-07-14
This name is really misleading as it isn't NTLM v2 authentication
rather this authentication is only used when the ntlm_compatibility
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"""
[MS-NLMP] v28.0 2016-07-14
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jborean93/ntlm-auth | ntlm_auth/compute_response.py | ComputeResponse._get_NTLMv2_response | def _get_NTLMv2_response(user_name, password, domain_name,
server_challenge, client_challenge, timestamp,
target_info):
"""
[MS-NLMP] v28.0 2016-07-14
2.2.2.8 NTLM V2 Response: NTLMv2_RESPONSE
The NTLMv2_RESPONSE strucutre define... | python | def _get_NTLMv2_response(user_name, password, domain_name,
server_challenge, client_challenge, timestamp,
target_info):
"""
[MS-NLMP] v28.0 2016-07-14
2.2.2.8 NTLM V2 Response: NTLMv2_RESPONSE
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jborean93/ntlm-auth | ntlm_auth/compute_response.py | ComputeResponse._get_NTLMv2_temp | def _get_NTLMv2_temp(timestamp, client_challenge, target_info):
"""
[MS-NLMP] v28.0 2016-07-14
2.2.2.7 NTLMv2_CLIENT_CHALLENGE - variable length
The NTLMv2_CLIENT_CHALLENGE structure defines the client challenge in
the AUTHENTICATE_MESSAGE. This structure is used only when NTLM ... | python | def _get_NTLMv2_temp(timestamp, client_challenge, target_info):
"""
[MS-NLMP] v28.0 2016-07-14
2.2.2.7 NTLMv2_CLIENT_CHALLENGE - variable length
The NTLMv2_CLIENT_CHALLENGE structure defines the client challenge in
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jborean93/ntlm-auth | ntlm_auth/compute_response.py | ComputeResponse._calc_resp | def _calc_resp(password_hash, server_challenge):
"""
Generate the LM response given a 16-byte password hash and the
challenge from the CHALLENGE_MESSAGE
:param password_hash: A 16-byte password hash
:param server_challenge: A random 8-byte response generated by the
s... | python | def _calc_resp(password_hash, server_challenge):
"""
Generate the LM response given a 16-byte password hash and the
challenge from the CHALLENGE_MESSAGE
:param password_hash: A 16-byte password hash
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jborean93/ntlm-auth | ntlm_auth/des.py | DES.encrypt | def encrypt(self, data, pad=True):
"""
DES encrypts the data based on the key it was initialised with.
:param data: The bytes string to encrypt
:param pad: Whether to right pad data with \x00 to a multiple of 8
:return: The encrypted bytes string
"""
encrypted_da... | python | def encrypt(self, data, pad=True):
"""
DES encrypts the data based on the key it was initialised with.
:param data: The bytes string to encrypt
:param pad: Whether to right pad data with \x00 to a multiple of 8
:return: The encrypted bytes string
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jborean93/ntlm-auth | ntlm_auth/des.py | DES.decrypt | def decrypt(self, data):
"""
DES decrypts the data based on the key it was initialised with.
:param data: The encrypted bytes string to decrypt
:return: The decrypted bytes string
"""
decrypted_data = b""
for i in range(0, len(data), 8):
block = data[... | python | def decrypt(self, data):
"""
DES decrypts the data based on the key it was initialised with.
:param data: The encrypted bytes string to decrypt
:return: The decrypted bytes string
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jborean93/ntlm-auth | ntlm_auth/des.py | DES.key56_to_key64 | def key56_to_key64(key):
"""
This takes in an a bytes string of 7 bytes and converts it to a bytes
string of 8 bytes with the odd parity bit being set to every 8 bits,
For example
b"\x01\x02\x03\x04\x05\x06\x07"
00000001 00000010 00000011 00000100 00000101 00000110 0000... | python | def key56_to_key64(key):
"""
This takes in an a bytes string of 7 bytes and converts it to a bytes
string of 8 bytes with the odd parity bit being set to every 8 bits,
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b"\x01\x02\x03\x04\x05\x06\x07"
00000001 00000010 00000011 00000100 00000101 00000110 0000... | [
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jborean93/ntlm-auth | ntlm_auth/compute_hash.py | _lmowfv1 | def _lmowfv1(password):
"""
[MS-NLMP] v28.0 2016-07-14
3.3.1 NTLM v1 Authentication
Same function as LMOWFv1 in document to create a one way hash of the
password. Only used in NTLMv1 auth without session security
:param password: The password or hash of the user we are trying to
authen... | python | def _lmowfv1(password):
"""
[MS-NLMP] v28.0 2016-07-14
3.3.1 NTLM v1 Authentication
Same function as LMOWFv1 in document to create a one way hash of the
password. Only used in NTLMv1 auth without session security
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jborean93/ntlm-auth | ntlm_auth/compute_hash.py | _ntowfv1 | def _ntowfv1(password):
"""
[MS-NLMP] v28.0 2016-07-14
3.3.1 NTLM v1 Authentication
Same function as NTOWFv1 in document to create a one way hash of the
password. Only used in NTLMv1 auth without session security
:param password: The password or hash of the user we are trying to
authen... | python | def _ntowfv1(password):
"""
[MS-NLMP] v28.0 2016-07-14
3.3.1 NTLM v1 Authentication
Same function as NTOWFv1 in document to create a one way hash of the
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jborean93/ntlm-auth | ntlm_auth/compute_hash.py | _ntowfv2 | def _ntowfv2(user_name, password, domain_name):
"""
[MS-NLMP] v28.0 2016-07-14
3.3.2 NTLM v2 Authentication
Same function as NTOWFv2 (and LMOWFv2) in document to create a one way hash
of the password. This combines some extra security features over the v1
calculations used in NTLMv2 auth.
... | python | def _ntowfv2(user_name, password, domain_name):
"""
[MS-NLMP] v28.0 2016-07-14
3.3.2 NTLM v2 Authentication
Same function as NTOWFv2 (and LMOWFv2) in document to create a one way hash
of the password. This combines some extra security features over the v1
calculations used in NTLMv2 auth.
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datawire/quark | quarkc/compiler.py | Check.visit_Method | def visit_Method(self, method):
"""
Ensure method has the same signature matching method on parent interface.
:param method: L{quarkc.ast.Method} instance.
"""
resolved_method = method.resolved.type
def get_params(method, extra_bindings):
# The Method should... | python | def visit_Method(self, method):
"""
Ensure method has the same signature matching method on parent interface.
:param method: L{quarkc.ast.Method} instance.
"""
resolved_method = method.resolved.type
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blacktop/virustotal-api | virus_total_apis/api.py | PublicApi.rescan_file | def rescan_file(self, this_hash, timeout=None):
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blacktop/virustotal-api | virus_total_apis/api.py | PrivateApi.get_upload_url | def get_upload_url(self, timeout=None):
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""" Get a special URL for submitted files bigger than 32MB.
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blacktop/virustotal-api | virus_total_apis/api.py | PrivateApi.rescan_file | def rescan_file(self, resource, date='', period='', repeat='', notify_url='', notify_changes_only='', timeout=None):
""" Rescan a previously submitted filed or schedule an scan to be performed in the future.
This API allows you to rescan files present in VirusTotal's file store without having to
... | python | def rescan_file(self, resource, date='', period='', repeat='', notify_url='', notify_changes_only='', timeout=None):
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blacktop/virustotal-api | virus_total_apis/api.py | PrivateApi.file_search | def file_search(self, query, offset=None, timeout=None):
""" Search for samples.
In addition to retrieving all information on a particular file, VirusTotal allows you to perform what we
call "advanced reverse searches". Reverse searches take you from a file property to a list of files that
... | python | def file_search(self, query, offset=None, timeout=None):
""" Search for samples.
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blacktop/virustotal-api | virus_total_apis/api.py | PrivateApi.get_file_clusters | def get_file_clusters(self, this_date, timeout=None):
""" File similarity clusters for a given time frame.
VirusTotal has built its own in-house file similarity clustering functionality. At present, this clustering
works only on PE, PDF, DOC and RTF files and is based on a very simple structura... | python | def get_file_clusters(self, this_date, timeout=None):
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blacktop/virustotal-api | virus_total_apis/api.py | PrivateApi.get_url_distribution | def get_url_distribution(self, after=None, reports='true', limit=1000, timeout=None):
""" Get a live feed with the lastest URLs submitted to VirusTotal.
Allows you to retrieve a live feed of URLs submitted to VirusTotal, along with their scan reports. This
call enables you to stay synced with V... | python | def get_url_distribution(self, after=None, reports='true', limit=1000, timeout=None):
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blacktop/virustotal-api | virus_total_apis/api.py | PrivateApi.get_url_feed | def get_url_feed(self, package=None, timeout=None):
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blacktop/virustotal-api | virus_total_apis/api.py | IntelApi.get_hashes_from_search | def get_hashes_from_search(self, query, page=None, timeout=None):
""" Get the scan results for a file.
Even if you do not have a Private Mass API key that you can use, you can still automate VirusTotal Intelligence
searches pretty much in the same way that the searching for files api call works... | python | def get_hashes_from_search(self, query, page=None, timeout=None):
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Even if you do not have a Private Mass API key that you can use, you can still automate VirusTotal Intelligence
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blacktop/virustotal-api | virus_total_apis/api.py | IntelApi.get_file | def get_file(self, file_hash, save_file_at, timeout=None):
""" Get the scan results for a file.
Even if you do not have a Private Mass API key that you can use, you can still download files from the
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blacktop/virustotal-api | virus_total_apis/api.py | IntelApi.get_all_file_report_pages | def get_all_file_report_pages(self, query):
""" Get File Report (All Pages).
:param query: a VirusTotal Intelligence search string in accordance with the file search documentation.
:return: All JSON responses appended together.
"""
responses = []
r = self.get_hashes_from... | python | def get_all_file_report_pages(self, query):
""" Get File Report (All Pages).
:param query: a VirusTotal Intelligence search string in accordance with the file search documentation.
:return: All JSON responses appended together.
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blacktop/virustotal-api | virus_total_apis/api.py | IntelApi.get_intel_notifications_feed | def get_intel_notifications_feed(self, page=None, timeout=None):
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blacktop/virustotal-api | virus_total_apis/api.py | IntelApi.delete_intel_notifications | def delete_intel_notifications(self, ids, timeout=None):
""" Programmatically delete notifications via the Intel API.
:param ids: A list of IDs to delete from the notification feed.
:returns: The post response.
"""
if not isinstance(ids, list):
raise TypeError("ids m... | python | def delete_intel_notifications(self, ids, timeout=None):
""" Programmatically delete notifications via the Intel API.
:param ids: A list of IDs to delete from the notification feed.
:returns: The post response.
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localstack/localstack-python-client | localstack_client/session.py | Session.get_credentials | def get_credentials(self):
"""
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"""
return Credentials(access_key=self.aws_access_key_id,
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fabric-bolt/fabric-bolt | fabric_bolt/core/mixins/views.py | MultipleGroupRequiredMixin.check_membership | def check_membership(self, group):
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user_groups = self.request.user.groups.values_list("name", flat=True)
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""" Check required group(s) """
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