repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_documentation_string stringlengths 1 47.2k | func_code_url stringlengths 85 339 |
|---|---|---|---|---|---|---|---|
klavinslab/coral | coral/sequence/_dna.py | DNA.ape | def ape(self, ape_path=None):
'''Open in ApE if `ApE` is in your command line path.'''
# TODO: simplify - make ApE look in PATH only
cmd = 'ApE'
if ape_path is None:
# Check for ApE in PATH
ape_executables = []
for path in os.environ['PATH'].split(os.p... | python | def ape(self, ape_path=None):
'''Open in ApE if `ApE` is in your command line path.'''
# TODO: simplify - make ApE look in PATH only
cmd = 'ApE'
if ape_path is None:
# Check for ApE in PATH
ape_executables = []
for path in os.environ['PATH'].split(os.p... | Open in ApE if `ApE` is in your command line path. | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L84-L111 |
klavinslab/coral | coral/sequence/_dna.py | DNA.copy | def copy(self):
'''Create a copy of the current instance.
:returns: A safely-editable copy of the current sequence.
:rtype: coral.DNA
'''
# Significant performance improvements by skipping alphabet check
features_copy = [feature.copy() for feature in self.features]
... | python | def copy(self):
'''Create a copy of the current instance.
:returns: A safely-editable copy of the current sequence.
:rtype: coral.DNA
'''
# Significant performance improvements by skipping alphabet check
features_copy = [feature.copy() for feature in self.features]
... | Create a copy of the current instance.
:returns: A safely-editable copy of the current sequence.
:rtype: coral.DNA | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L113-L125 |
klavinslab/coral | coral/sequence/_dna.py | DNA.circularize | def circularize(self):
'''Circularize linear DNA.
:returns: A circularized version of the current sequence.
:rtype: coral.DNA
'''
if self.top[-1].seq == '-' and self.bottom[0].seq == '-':
raise ValueError('Cannot circularize - termini disconnected.')
if self... | python | def circularize(self):
'''Circularize linear DNA.
:returns: A circularized version of the current sequence.
:rtype: coral.DNA
'''
if self.top[-1].seq == '-' and self.bottom[0].seq == '-':
raise ValueError('Cannot circularize - termini disconnected.')
if self... | Circularize linear DNA.
:returns: A circularized version of the current sequence.
:rtype: coral.DNA | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L127-L143 |
klavinslab/coral | coral/sequence/_dna.py | DNA.display | def display(self):
'''Display a visualization of the sequence in an IPython notebook.'''
try:
from IPython.display import HTML
import uuid
except ImportError:
raise IPythonDisplayImportError
sequence_json = self.json()
d3cdn = '//d3js.org/d3.... | python | def display(self):
'''Display a visualization of the sequence in an IPython notebook.'''
try:
from IPython.display import HTML
import uuid
except ImportError:
raise IPythonDisplayImportError
sequence_json = self.json()
d3cdn = '//d3js.org/d3.... | Display a visualization of the sequence in an IPython notebook. | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L145-L176 |
klavinslab/coral | coral/sequence/_dna.py | DNA.excise | def excise(self, feature):
'''Removes feature from circular plasmid and linearizes. Automatically
reorients at the base just after the feature. This operation is
complementary to the .extract() method.
:param feature_name: The feature to remove.
:type feature_name: coral.Feature... | python | def excise(self, feature):
'''Removes feature from circular plasmid and linearizes. Automatically
reorients at the base just after the feature. This operation is
complementary to the .extract() method.
:param feature_name: The feature to remove.
:type feature_name: coral.Feature... | Removes feature from circular plasmid and linearizes. Automatically
reorients at the base just after the feature. This operation is
complementary to the .extract() method.
:param feature_name: The feature to remove.
:type feature_name: coral.Feature | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L202-L214 |
klavinslab/coral | coral/sequence/_dna.py | DNA.extract | def extract(self, feature, remove_subfeatures=False):
'''Extract a feature from the sequence. This operation is complementary
to the .excise() method.
:param feature: Feature object.
:type feature: coral.sequence.Feature
:param remove_subfeatures: Remove all features in the extr... | python | def extract(self, feature, remove_subfeatures=False):
'''Extract a feature from the sequence. This operation is complementary
to the .excise() method.
:param feature: Feature object.
:type feature: coral.sequence.Feature
:param remove_subfeatures: Remove all features in the extr... | Extract a feature from the sequence. This operation is complementary
to the .excise() method.
:param feature: Feature object.
:type feature: coral.sequence.Feature
:param remove_subfeatures: Remove all features in the extracted
sequence aside from the ... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L216-L240 |
klavinslab/coral | coral/sequence/_dna.py | DNA.flip | def flip(self):
'''Flip the DNA - swap the top and bottom strands.
:returns: Flipped DNA (bottom strand is now top strand, etc.).
:rtype: coral.DNA
'''
copy = self.copy()
copy.top, copy.bottom = copy.bottom, copy.top
copy.features = [_flip_feature(f, len(self)) ... | python | def flip(self):
'''Flip the DNA - swap the top and bottom strands.
:returns: Flipped DNA (bottom strand is now top strand, etc.).
:rtype: coral.DNA
'''
copy = self.copy()
copy.top, copy.bottom = copy.bottom, copy.top
copy.features = [_flip_feature(f, len(self)) ... | Flip the DNA - swap the top and bottom strands.
:returns: Flipped DNA (bottom strand is now top strand, etc.).
:rtype: coral.DNA | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L242-L252 |
klavinslab/coral | coral/sequence/_dna.py | DNA.linearize | def linearize(self, index=0):
'''Linearize circular DNA at an index.
:param index: index at which to linearize.
:type index: int
:returns: A linearized version of the current sequence.
:rtype: coral.DNA
:raises: ValueError if the input is linear DNA.
'''
... | python | def linearize(self, index=0):
'''Linearize circular DNA at an index.
:param index: index at which to linearize.
:type index: int
:returns: A linearized version of the current sequence.
:rtype: coral.DNA
:raises: ValueError if the input is linear DNA.
'''
... | Linearize circular DNA at an index.
:param index: index at which to linearize.
:type index: int
:returns: A linearized version of the current sequence.
:rtype: coral.DNA
:raises: ValueError if the input is linear DNA. | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L275-L295 |
klavinslab/coral | coral/sequence/_dna.py | DNA.locate | def locate(self, pattern):
'''Find sequences matching a pattern. For a circular sequence, the
search extends over the origin.
:param pattern: str or NucleicAcidSequence for which to find matches.
:type pattern: str or coral.DNA
:returns: A list of top and bottom strand indices o... | python | def locate(self, pattern):
'''Find sequences matching a pattern. For a circular sequence, the
search extends over the origin.
:param pattern: str or NucleicAcidSequence for which to find matches.
:type pattern: str or coral.DNA
:returns: A list of top and bottom strand indices o... | Find sequences matching a pattern. For a circular sequence, the
search extends over the origin.
:param pattern: str or NucleicAcidSequence for which to find matches.
:type pattern: str or coral.DNA
:returns: A list of top and bottom strand indices of matches.
:rtype: list of lis... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L297-L313 |
klavinslab/coral | coral/sequence/_dna.py | DNA.rotate | def rotate(self, n):
'''Rotate Sequence by n bases.
:param n: Number of bases to rotate.
:type n: int
:returns: The current sequence reoriented at `index`.
:rtype: coral.DNA
:raises: ValueError if applied to linear sequence or `index` is
negative.
... | python | def rotate(self, n):
'''Rotate Sequence by n bases.
:param n: Number of bases to rotate.
:type n: int
:returns: The current sequence reoriented at `index`.
:rtype: coral.DNA
:raises: ValueError if applied to linear sequence or `index` is
negative.
... | Rotate Sequence by n bases.
:param n: Number of bases to rotate.
:type n: int
:returns: The current sequence reoriented at `index`.
:rtype: coral.DNA
:raises: ValueError if applied to linear sequence or `index` is
negative. | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L324-L350 |
klavinslab/coral | coral/sequence/_dna.py | DNA.reverse_complement | def reverse_complement(self):
'''Reverse complement the DNA.
:returns: A reverse-complemented instance of the current sequence.
:rtype: coral.DNA
'''
copy = self.copy()
# Note: if sequence is double-stranded, swapping strand is basically
# (but not entirely) the... | python | def reverse_complement(self):
'''Reverse complement the DNA.
:returns: A reverse-complemented instance of the current sequence.
:rtype: coral.DNA
'''
copy = self.copy()
# Note: if sequence is double-stranded, swapping strand is basically
# (but not entirely) the... | Reverse complement the DNA.
:returns: A reverse-complemented instance of the current sequence.
:rtype: coral.DNA | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L379-L395 |
klavinslab/coral | coral/sequence/_dna.py | DNA.select_features | def select_features(self, term, by='name', fuzzy=False):
'''Select features from the features list based on feature name,
gene, or locus tag.
:param term: Search term.
:type term: str
:param by: Feature attribute to search by. Options are 'name',
'gene', an... | python | def select_features(self, term, by='name', fuzzy=False):
'''Select features from the features list based on feature name,
gene, or locus tag.
:param term: Search term.
:type term: str
:param by: Feature attribute to search by. Options are 'name',
'gene', an... | Select features from the features list based on feature name,
gene, or locus tag.
:param term: Search term.
:type term: str
:param by: Feature attribute to search by. Options are 'name',
'gene', and 'locus_tag'.
:type by: str
:param fuzzy: If ... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L397-L424 |
klavinslab/coral | coral/sequence/_dna.py | DNA.to_feature | def to_feature(self, name=None, feature_type='misc_feature'):
'''Create a feature from the current object.
:param name: Name for the new feature. Must be specified if the DNA
instance has no .name attribute.
:type name: str
:param feature_type: The type of feature (... | python | def to_feature(self, name=None, feature_type='misc_feature'):
'''Create a feature from the current object.
:param name: Name for the new feature. Must be specified if the DNA
instance has no .name attribute.
:type name: str
:param feature_type: The type of feature (... | Create a feature from the current object.
:param name: Name for the new feature. Must be specified if the DNA
instance has no .name attribute.
:type name: str
:param feature_type: The type of feature (genbank standard).
:type feature_type: str | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L436-L452 |
klavinslab/coral | coral/sequence/_dna.py | RestrictionSite.cuts_outside | def cuts_outside(self):
'''Report whether the enzyme cuts outside its recognition site.
Cutting at the very end of the site returns True.
:returns: Whether the enzyme will cut outside its recognition site.
:rtype: bool
'''
for index in self.cut_site:
if inde... | python | def cuts_outside(self):
'''Report whether the enzyme cuts outside its recognition site.
Cutting at the very end of the site returns True.
:returns: Whether the enzyme will cut outside its recognition site.
:rtype: bool
'''
for index in self.cut_site:
if inde... | Report whether the enzyme cuts outside its recognition site.
Cutting at the very end of the site returns True.
:returns: Whether the enzyme will cut outside its recognition site.
:rtype: bool | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L787-L798 |
klavinslab/coral | coral/sequence/_dna.py | Primer.copy | def copy(self):
'''Generate a Primer copy.
:returns: A safely-editable copy of the current primer.
:rtype: coral.DNA
'''
return type(self)(self.anneal, self.tm, overhang=self.overhang,
name=self.name, note=self.note) | python | def copy(self):
'''Generate a Primer copy.
:returns: A safely-editable copy of the current primer.
:rtype: coral.DNA
'''
return type(self)(self.anneal, self.tm, overhang=self.overhang,
name=self.name, note=self.note) | Generate a Primer copy.
:returns: A safely-editable copy of the current primer.
:rtype: coral.DNA | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_dna.py#L886-L894 |
klavinslab/coral | coral/analysis/_sequence/melting_temp.py | tm | def tm(seq, dna_conc=50, salt_conc=50, parameters='cloning'):
'''Calculate nearest-neighbor melting temperature (Tm).
:param seq: Sequence for which to calculate the tm.
:type seq: coral.DNA
:param dna_conc: DNA concentration in nM.
:type dna_conc: float
:param salt_conc: Salt concentration in ... | python | def tm(seq, dna_conc=50, salt_conc=50, parameters='cloning'):
'''Calculate nearest-neighbor melting temperature (Tm).
:param seq: Sequence for which to calculate the tm.
:type seq: coral.DNA
:param dna_conc: DNA concentration in nM.
:type dna_conc: float
:param salt_conc: Salt concentration in ... | Calculate nearest-neighbor melting temperature (Tm).
:param seq: Sequence for which to calculate the tm.
:type seq: coral.DNA
:param dna_conc: DNA concentration in nM.
:type dna_conc: float
:param salt_conc: Salt concentration in mM.
:type salt_conc: float
:param parameters: Nearest-neighbo... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequence/melting_temp.py#L22-L144 |
klavinslab/coral | coral/analysis/_sequence/melting_temp.py | _pair_deltas | def _pair_deltas(seq, pars):
'''Add up nearest-neighbor parameters for a given sequence.
:param seq: DNA sequence for which to sum nearest neighbors
:type seq: str
:param pars: parameter set to use
:type pars: dict
:returns: nearest-neighbor delta_H and delta_S sums.
:rtype: tuple of floats... | python | def _pair_deltas(seq, pars):
'''Add up nearest-neighbor parameters for a given sequence.
:param seq: DNA sequence for which to sum nearest neighbors
:type seq: str
:param pars: parameter set to use
:type pars: dict
:returns: nearest-neighbor delta_H and delta_S sums.
:rtype: tuple of floats... | Add up nearest-neighbor parameters for a given sequence.
:param seq: DNA sequence for which to sum nearest neighbors
:type seq: str
:param pars: parameter set to use
:type pars: dict
:returns: nearest-neighbor delta_H and delta_S sums.
:rtype: tuple of floats | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequence/melting_temp.py#L147-L164 |
klavinslab/coral | coral/analysis/_sequence/melting_temp.py | breslauer_corrections | def breslauer_corrections(seq, pars_error):
'''Sum corrections for Breslauer '84 method.
:param seq: sequence for which to calculate corrections.
:type seq: str
:param pars_error: dictionary of error corrections
:type pars_error: dict
:returns: Corrected delta_H and delta_S parameters
:rtyp... | python | def breslauer_corrections(seq, pars_error):
'''Sum corrections for Breslauer '84 method.
:param seq: sequence for which to calculate corrections.
:type seq: str
:param pars_error: dictionary of error corrections
:type pars_error: dict
:returns: Corrected delta_H and delta_S parameters
:rtyp... | Sum corrections for Breslauer '84 method.
:param seq: sequence for which to calculate corrections.
:type seq: str
:param pars_error: dictionary of error corrections
:type pars_error: dict
:returns: Corrected delta_H and delta_S parameters
:rtype: list of floats | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequence/melting_temp.py#L167-L193 |
klavinslab/coral | coral/analysis/_sequence/melting_temp.py | santalucia98_corrections | def santalucia98_corrections(seq, pars_error):
'''Sum corrections for SantaLucia '98 method (unified parameters).
:param seq: sequence for which to calculate corrections.
:type seq: str
:param pars_error: dictionary of error corrections
:type pars_error: dict
:returns: Corrected delta_H and del... | python | def santalucia98_corrections(seq, pars_error):
'''Sum corrections for SantaLucia '98 method (unified parameters).
:param seq: sequence for which to calculate corrections.
:type seq: str
:param pars_error: dictionary of error corrections
:type pars_error: dict
:returns: Corrected delta_H and del... | Sum corrections for SantaLucia '98 method (unified parameters).
:param seq: sequence for which to calculate corrections.
:type seq: str
:param pars_error: dictionary of error corrections
:type pars_error: dict
:returns: Corrected delta_H and delta_S parameters
:rtype: list of floats | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequence/melting_temp.py#L196-L225 |
klavinslab/coral | coral/analysis/_sequencing/mafft.py | MAFFT | def MAFFT(sequences, gap_open=1.53, gap_extension=0.0, retree=2):
'''A Coral wrapper for the MAFFT command line multiple sequence aligner.
:param sequences: A list of sequences to align.
:type sequences: List of homogeneous sequences (all DNA, or all RNA,
etc.)
:param gap_open: --o... | python | def MAFFT(sequences, gap_open=1.53, gap_extension=0.0, retree=2):
'''A Coral wrapper for the MAFFT command line multiple sequence aligner.
:param sequences: A list of sequences to align.
:type sequences: List of homogeneous sequences (all DNA, or all RNA,
etc.)
:param gap_open: --o... | A Coral wrapper for the MAFFT command line multiple sequence aligner.
:param sequences: A list of sequences to align.
:type sequences: List of homogeneous sequences (all DNA, or all RNA,
etc.)
:param gap_open: --op (gap open) penalty in MAFFT cli.
:type gap_open: float
:param g... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequencing/mafft.py#L9-L55 |
klavinslab/coral | coral/analysis/_sequence/repeats.py | repeats | def repeats(seq, size):
'''Count times that a sequence of a certain size is repeated.
:param seq: Input sequence.
:type seq: coral.DNA or coral.RNA
:param size: Size of the repeat to count.
:type size: int
:returns: Occurrences of repeats and how many
:rtype: tuple of the matched sequence a... | python | def repeats(seq, size):
'''Count times that a sequence of a certain size is repeated.
:param seq: Input sequence.
:type seq: coral.DNA or coral.RNA
:param size: Size of the repeat to count.
:type size: int
:returns: Occurrences of repeats and how many
:rtype: tuple of the matched sequence a... | Count times that a sequence of a certain size is repeated.
:param seq: Input sequence.
:type seq: coral.DNA or coral.RNA
:param size: Size of the repeat to count.
:type size: int
:returns: Occurrences of repeats and how many
:rtype: tuple of the matched sequence and how many times it occurs | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequence/repeats.py#L5-L22 |
klavinslab/coral | coral/reaction/_gibson.py | gibson | def gibson(seq_list, linear=False, homology=10, tm=63.0):
'''Simulate a Gibson reaction.
:param seq_list: list of DNA sequences to Gibson
:type seq_list: list of coral.DNA
:param linear: Attempt to produce linear, rather than circular,
fragment from input fragments.
:type linear:... | python | def gibson(seq_list, linear=False, homology=10, tm=63.0):
'''Simulate a Gibson reaction.
:param seq_list: list of DNA sequences to Gibson
:type seq_list: list of coral.DNA
:param linear: Attempt to produce linear, rather than circular,
fragment from input fragments.
:type linear:... | Simulate a Gibson reaction.
:param seq_list: list of DNA sequences to Gibson
:type seq_list: list of coral.DNA
:param linear: Attempt to produce linear, rather than circular,
fragment from input fragments.
:type linear: bool
:param homology_min: minimum bp of homology allowed
... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/reaction/_gibson.py#L21-L60 |
klavinslab/coral | coral/reaction/_gibson.py | _find_fuse_next | def _find_fuse_next(working_list, homology, tm):
'''Find the next sequence to fuse, and fuse it (or raise exception).
:param homology: length of terminal homology in bp
:type homology: int
:raises: AmbiguousGibsonError if there is more than one way for the
fragment ends to combine.
... | python | def _find_fuse_next(working_list, homology, tm):
'''Find the next sequence to fuse, and fuse it (or raise exception).
:param homology: length of terminal homology in bp
:type homology: int
:raises: AmbiguousGibsonError if there is more than one way for the
fragment ends to combine.
... | Find the next sequence to fuse, and fuse it (or raise exception).
:param homology: length of terminal homology in bp
:type homology: int
:raises: AmbiguousGibsonError if there is more than one way for the
fragment ends to combine.
GibsonOverlapError if no homology match can be fou... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/reaction/_gibson.py#L87-L150 |
klavinslab/coral | coral/reaction/_gibson.py | _fuse_last | def _fuse_last(working_list, homology, tm):
'''With one sequence left, attempt to fuse it to itself.
:param homology: length of terminal homology in bp.
:type homology: int
:raises: AmbiguousGibsonError if either of the termini are palindromic
(would bind self-self).
ValueErro... | python | def _fuse_last(working_list, homology, tm):
'''With one sequence left, attempt to fuse it to itself.
:param homology: length of terminal homology in bp.
:type homology: int
:raises: AmbiguousGibsonError if either of the termini are palindromic
(would bind self-self).
ValueErro... | With one sequence left, attempt to fuse it to itself.
:param homology: length of terminal homology in bp.
:type homology: int
:raises: AmbiguousGibsonError if either of the termini are palindromic
(would bind self-self).
ValueError if the ends are not compatible. | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/reaction/_gibson.py#L153-L191 |
klavinslab/coral | coral/reaction/_gibson.py | homology_report | def homology_report(seq1, seq2, strand1, strand2, cutoff=0, min_tm=63.0,
top_two=False, max_size=500):
'''Given two sequences (seq1 and seq2), report the size of all perfect
matches between the 3' end of the top strand of seq1 and the 3' end of
either strand of seq2. In short, in a Gibso... | python | def homology_report(seq1, seq2, strand1, strand2, cutoff=0, min_tm=63.0,
top_two=False, max_size=500):
'''Given two sequences (seq1 and seq2), report the size of all perfect
matches between the 3' end of the top strand of seq1 and the 3' end of
either strand of seq2. In short, in a Gibso... | Given two sequences (seq1 and seq2), report the size of all perfect
matches between the 3' end of the top strand of seq1 and the 3' end of
either strand of seq2. In short, in a Gibson reaction, what would bind the
desired part of seq1, given a seq2?
:param seq1: Sequence for which to test 3\' binding o... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/reaction/_gibson.py#L194-L270 |
klavinslab/coral | coral/database/_yeast.py | fetch_yeast_locus_sequence | def fetch_yeast_locus_sequence(locus_name, flanking_size=0):
'''Acquire a sequence from SGD http://www.yeastgenome.org.
:param locus_name: Common name or systematic name for the locus (e.g. ACT1
or YFL039C).
:type locus_name: str
:param flanking_size: The length of flanking DNA (... | python | def fetch_yeast_locus_sequence(locus_name, flanking_size=0):
'''Acquire a sequence from SGD http://www.yeastgenome.org.
:param locus_name: Common name or systematic name for the locus (e.g. ACT1
or YFL039C).
:type locus_name: str
:param flanking_size: The length of flanking DNA (... | Acquire a sequence from SGD http://www.yeastgenome.org.
:param locus_name: Common name or systematic name for the locus (e.g. ACT1
or YFL039C).
:type locus_name: str
:param flanking_size: The length of flanking DNA (on each side) to return
:type flanking_size: int | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/database/_yeast.py#L6-L83 |
klavinslab/coral | coral/database/_yeast.py | get_yeast_sequence | def get_yeast_sequence(chromosome, start, end, reverse_complement=False):
'''Acquire a sequence from SGD http://www.yeastgenome.org
:param chromosome: Yeast chromosome.
:type chromosome: int
:param start: A biostart.
:type start: int
:param end: A bioend.
:type end: int
:param reverse_co... | python | def get_yeast_sequence(chromosome, start, end, reverse_complement=False):
'''Acquire a sequence from SGD http://www.yeastgenome.org
:param chromosome: Yeast chromosome.
:type chromosome: int
:param start: A biostart.
:type start: int
:param end: A bioend.
:type end: int
:param reverse_co... | Acquire a sequence from SGD http://www.yeastgenome.org
:param chromosome: Yeast chromosome.
:type chromosome: int
:param start: A biostart.
:type start: int
:param end: A bioend.
:type end: int
:param reverse_complement: Get the reverse complement.
:type revervse_complement: bool
:re... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/database/_yeast.py#L86-L126 |
klavinslab/coral | coral/database/_yeast.py | get_yeast_gene_location | def get_yeast_gene_location(gene_name):
'''Acquire the location of a gene from SGD http://www.yeastgenome.org
:param gene_name: Name of the gene.
:type gene_name: string
:returns location: [int: chromosome, int:biostart, int:bioend, int:strand]
:rtype location: list
'''
from intermine.webse... | python | def get_yeast_gene_location(gene_name):
'''Acquire the location of a gene from SGD http://www.yeastgenome.org
:param gene_name: Name of the gene.
:type gene_name: string
:returns location: [int: chromosome, int:biostart, int:bioend, int:strand]
:rtype location: list
'''
from intermine.webse... | Acquire the location of a gene from SGD http://www.yeastgenome.org
:param gene_name: Name of the gene.
:type gene_name: string
:returns location: [int: chromosome, int:biostart, int:bioend, int:strand]
:rtype location: list | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/database/_yeast.py#L129-L182 |
klavinslab/coral | coral/database/_yeast.py | get_gene_id | def get_gene_id(gene_name):
'''Retrieve systematic yeast gene name from the common name.
:param gene_name: Common name for yeast gene (e.g. ADE2).
:type gene_name: str
:returns: Systematic name for yeast gene (e.g. YOR128C).
:rtype: str
'''
from intermine.webservice import Service
ser... | python | def get_gene_id(gene_name):
'''Retrieve systematic yeast gene name from the common name.
:param gene_name: Common name for yeast gene (e.g. ADE2).
:type gene_name: str
:returns: Systematic name for yeast gene (e.g. YOR128C).
:rtype: str
'''
from intermine.webservice import Service
ser... | Retrieve systematic yeast gene name from the common name.
:param gene_name: Common name for yeast gene (e.g. ADE2).
:type gene_name: str
:returns: Systematic name for yeast gene (e.g. YOR128C).
:rtype: str | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/database/_yeast.py#L185-L219 |
klavinslab/coral | coral/database/_yeast.py | get_yeast_promoter_ypa | def get_yeast_promoter_ypa(gene_name):
'''Retrieve promoter from Yeast Promoter Atlas
(http://ypa.csbb.ntu.edu.tw).
:param gene_name: Common name for yeast gene.
:type gene_name: str
:returns: Double-stranded DNA sequence of the promoter.
:rtype: coral.DNA
'''
import requests
loc ... | python | def get_yeast_promoter_ypa(gene_name):
'''Retrieve promoter from Yeast Promoter Atlas
(http://ypa.csbb.ntu.edu.tw).
:param gene_name: Common name for yeast gene.
:type gene_name: str
:returns: Double-stranded DNA sequence of the promoter.
:rtype: coral.DNA
'''
import requests
loc ... | Retrieve promoter from Yeast Promoter Atlas
(http://ypa.csbb.ntu.edu.tw).
:param gene_name: Common name for yeast gene.
:type gene_name: str
:returns: Double-stranded DNA sequence of the promoter.
:rtype: coral.DNA | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/database/_yeast.py#L222-L259 |
klavinslab/coral | coral/design/_oligo_synthesis/oligo_assembly.py | _grow_overlaps | def _grow_overlaps(dna, melting_temp, require_even, length_max, overlap_min,
min_exception):
'''Grows equidistant overlaps until they meet specified constraints.
:param dna: Input sequence.
:type dna: coral.DNA
:param melting_temp: Ideal Tm of the overlaps, in degrees C.
:type me... | python | def _grow_overlaps(dna, melting_temp, require_even, length_max, overlap_min,
min_exception):
'''Grows equidistant overlaps until they meet specified constraints.
:param dna: Input sequence.
:type dna: coral.DNA
:param melting_temp: Ideal Tm of the overlaps, in degrees C.
:type me... | Grows equidistant overlaps until they meet specified constraints.
:param dna: Input sequence.
:type dna: coral.DNA
:param melting_temp: Ideal Tm of the overlaps, in degrees C.
:type melting_temp: float
:param require_even: Require that the number of oligonucleotides is even.
:type require_even:... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_oligo_synthesis/oligo_assembly.py#L215-L347 |
klavinslab/coral | coral/design/_oligo_synthesis/oligo_assembly.py | _recalculate_overlaps | def _recalculate_overlaps(dna, overlaps, oligo_indices):
'''Recalculate overlap sequences based on the current overlap indices.
:param dna: Sequence being split into oligos.
:type dna: coral.DNA
:param overlaps: Current overlaps - a list of DNA sequences.
:type overlaps: coral.DNA list
:param o... | python | def _recalculate_overlaps(dna, overlaps, oligo_indices):
'''Recalculate overlap sequences based on the current overlap indices.
:param dna: Sequence being split into oligos.
:type dna: coral.DNA
:param overlaps: Current overlaps - a list of DNA sequences.
:type overlaps: coral.DNA list
:param o... | Recalculate overlap sequences based on the current overlap indices.
:param dna: Sequence being split into oligos.
:type dna: coral.DNA
:param overlaps: Current overlaps - a list of DNA sequences.
:type overlaps: coral.DNA list
:param oligo_indices: List of oligo indices (starts and stops).
:typ... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_oligo_synthesis/oligo_assembly.py#L350-L369 |
klavinslab/coral | coral/design/_oligo_synthesis/oligo_assembly.py | _expand_overlap | def _expand_overlap(dna, oligo_indices, index, oligos, length_max):
'''Given an overlap to increase, increases smaller oligo.
:param dna: Sequence being split into oligos.
:type dna: coral.DNA
:param oligo_indices: index of oligo starts and stops
:type oligo_indices: list
:param index: index of... | python | def _expand_overlap(dna, oligo_indices, index, oligos, length_max):
'''Given an overlap to increase, increases smaller oligo.
:param dna: Sequence being split into oligos.
:type dna: coral.DNA
:param oligo_indices: index of oligo starts and stops
:type oligo_indices: list
:param index: index of... | Given an overlap to increase, increases smaller oligo.
:param dna: Sequence being split into oligos.
:type dna: coral.DNA
:param oligo_indices: index of oligo starts and stops
:type oligo_indices: list
:param index: index of the oligo
:type index: int
:param left_len: length of left oligo
... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_oligo_synthesis/oligo_assembly.py#L372-L409 |
klavinslab/coral | coral/design/_oligo_synthesis/oligo_assembly.py | _adjust_overlap | def _adjust_overlap(positions_list, index, direction):
'''Increase overlap to the right or left of an index.
:param positions_list: list of overlap positions
:type positions_list: list
:param index: index of the overlap to increase.
:type index: int
:param direction: which side of the overlap t... | python | def _adjust_overlap(positions_list, index, direction):
'''Increase overlap to the right or left of an index.
:param positions_list: list of overlap positions
:type positions_list: list
:param index: index of the overlap to increase.
:type index: int
:param direction: which side of the overlap t... | Increase overlap to the right or left of an index.
:param positions_list: list of overlap positions
:type positions_list: list
:param index: index of the overlap to increase.
:type index: int
:param direction: which side of the overlap to increase - left or right.
:type direction: str
:retu... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_oligo_synthesis/oligo_assembly.py#L412-L432 |
klavinslab/coral | coral/design/_oligo_synthesis/oligo_assembly.py | OligoAssembly.design_assembly | def design_assembly(self):
'''Design the overlapping oligos.
:returns: Assembly oligos, and the sequences, Tms, and indices of their
overlapping regions.
:rtype: dict
'''
# Input parameters needed to design the oligos
length_range = self.kwargs['length... | python | def design_assembly(self):
'''Design the overlapping oligos.
:returns: Assembly oligos, and the sequences, Tms, and indices of their
overlapping regions.
:rtype: dict
'''
# Input parameters needed to design the oligos
length_range = self.kwargs['length... | Design the overlapping oligos.
:returns: Assembly oligos, and the sequences, Tms, and indices of their
overlapping regions.
:rtype: dict | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_oligo_synthesis/oligo_assembly.py#L57-L145 |
klavinslab/coral | coral/design/_oligo_synthesis/oligo_assembly.py | OligoAssembly.primers | def primers(self, tm=60):
'''Design primers for amplifying the assembled sequence.
:param tm: melting temperature (lower than overlaps is best).
:type tm: float
:returns: Primer list (the output of coral.design.primers).
:rtype: list
'''
self.primers = coral.des... | python | def primers(self, tm=60):
'''Design primers for amplifying the assembled sequence.
:param tm: melting temperature (lower than overlaps is best).
:type tm: float
:returns: Primer list (the output of coral.design.primers).
:rtype: list
'''
self.primers = coral.des... | Design primers for amplifying the assembled sequence.
:param tm: melting temperature (lower than overlaps is best).
:type tm: float
:returns: Primer list (the output of coral.design.primers).
:rtype: list | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_oligo_synthesis/oligo_assembly.py#L147-L157 |
klavinslab/coral | coral/design/_oligo_synthesis/oligo_assembly.py | OligoAssembly.write | def write(self, path):
'''Write assembly oligos and (if applicable) primers to csv.
:param path: path to csv file, including .csv extension.
:type path: str
'''
with open(path, 'wb') as oligo_file:
oligo_writer = csv.writer(oligo_file, delimiter=',',
... | python | def write(self, path):
'''Write assembly oligos and (if applicable) primers to csv.
:param path: path to csv file, including .csv extension.
:type path: str
'''
with open(path, 'wb') as oligo_file:
oligo_writer = csv.writer(oligo_file, delimiter=',',
... | Write assembly oligos and (if applicable) primers to csv.
:param path: path to csv file, including .csv extension.
:type path: str | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_oligo_synthesis/oligo_assembly.py#L159-L184 |
klavinslab/coral | coral/design/_oligo_synthesis/oligo_assembly.py | OligoAssembly.write_map | def write_map(self, path):
'''Write genbank map that highlights overlaps.
:param path: full path to .gb file to write.
:type path: str
'''
starts = [index[0] for index in self.overlap_indices]
features = []
for i, start in enumerate(starts):
stop = s... | python | def write_map(self, path):
'''Write genbank map that highlights overlaps.
:param path: full path to .gb file to write.
:type path: str
'''
starts = [index[0] for index in self.overlap_indices]
features = []
for i, start in enumerate(starts):
stop = s... | Write genbank map that highlights overlaps.
:param path: full path to .gb file to write.
:type path: str | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/design/_oligo_synthesis/oligo_assembly.py#L186-L203 |
klavinslab/coral | coral/reaction/_central_dogma.py | coding_sequence | def coding_sequence(rna):
'''Extract coding sequence from an RNA template.
:param seq: Sequence from which to extract a coding sequence.
:type seq: coral.RNA
:param material: Type of sequence ('dna' or 'rna')
:type material: str
:returns: The first coding sequence (start codon -> stop codon) ma... | python | def coding_sequence(rna):
'''Extract coding sequence from an RNA template.
:param seq: Sequence from which to extract a coding sequence.
:type seq: coral.RNA
:param material: Type of sequence ('dna' or 'rna')
:type material: str
:returns: The first coding sequence (start codon -> stop codon) ma... | Extract coding sequence from an RNA template.
:param seq: Sequence from which to extract a coding sequence.
:type seq: coral.RNA
:param material: Type of sequence ('dna' or 'rna')
:type material: str
:returns: The first coding sequence (start codon -> stop codon) matched
from 5' to 3'... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/reaction/_central_dogma.py#L42-L86 |
klavinslab/coral | coral/database/_rebase.py | Rebase.update | def update(self):
'''Update definitions.'''
# Download http://rebase.neb.com/rebase/link_withref to tmp
self._tmpdir = tempfile.mkdtemp()
try:
self._rebase_file = self._tmpdir + '/rebase_file'
print 'Downloading latest enzyme definitions'
url = 'http:/... | python | def update(self):
'''Update definitions.'''
# Download http://rebase.neb.com/rebase/link_withref to tmp
self._tmpdir = tempfile.mkdtemp()
try:
self._rebase_file = self._tmpdir + '/rebase_file'
print 'Downloading latest enzyme definitions'
url = 'http:/... | Update definitions. | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/database/_rebase.py#L15-L51 |
klavinslab/coral | coral/database/_rebase.py | Rebase._process_file | def _process_file(self):
'''Process rebase file into dict with name and cut site information.'''
print 'Processing file'
with open(self._rebase_file, 'r') as f:
raw = f.readlines()
names = [line.strip()[3:] for line in raw if line.startswith('<1>')]
seqs = [line.strip... | python | def _process_file(self):
'''Process rebase file into dict with name and cut site information.'''
print 'Processing file'
with open(self._rebase_file, 'r') as f:
raw = f.readlines()
names = [line.strip()[3:] for line in raw if line.startswith('<1>')]
seqs = [line.strip... | Process rebase file into dict with name and cut site information. | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/database/_rebase.py#L69-L102 |
klavinslab/coral | coral/sequence/_peptide.py | Peptide.copy | def copy(self):
'''Create a copy of the current instance.
:returns: A safely editable copy of the current sequence.
:rtype: coral.Peptide
'''
return type(self)(str(self._sequence), features=self.features,
run_checks=False) | python | def copy(self):
'''Create a copy of the current instance.
:returns: A safely editable copy of the current sequence.
:rtype: coral.Peptide
'''
return type(self)(str(self._sequence), features=self.features,
run_checks=False) | Create a copy of the current instance.
:returns: A safely editable copy of the current sequence.
:rtype: coral.Peptide | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_peptide.py#L26-L34 |
klavinslab/coral | coral/utils/tempdirs.py | tempdir | def tempdir(fun):
'''For use as a decorator of instance methods - creates a temporary dir
named self._tempdir and then deletes it after the method runs.
:param fun: function to decorate
:type fun: instance method
'''
def wrapper(*args, **kwargs):
self = args[0]
if os.path.isdir... | python | def tempdir(fun):
'''For use as a decorator of instance methods - creates a temporary dir
named self._tempdir and then deletes it after the method runs.
:param fun: function to decorate
:type fun: instance method
'''
def wrapper(*args, **kwargs):
self = args[0]
if os.path.isdir... | For use as a decorator of instance methods - creates a temporary dir
named self._tempdir and then deletes it after the method runs.
:param fun: function to decorate
:type fun: instance method | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/utils/tempdirs.py#L9-L30 |
klavinslab/coral | coral/reaction/utils.py | convert_sequence | def convert_sequence(seq, to_material):
'''Translate a DNA sequence into peptide sequence.
The following conversions are supported:
Transcription (seq is DNA, to_material is 'rna')
Reverse transcription (seq is RNA, to_material is 'dna')
Translation (seq is RNA, to_material is 'peptide'... | python | def convert_sequence(seq, to_material):
'''Translate a DNA sequence into peptide sequence.
The following conversions are supported:
Transcription (seq is DNA, to_material is 'rna')
Reverse transcription (seq is RNA, to_material is 'dna')
Translation (seq is RNA, to_material is 'peptide'... | Translate a DNA sequence into peptide sequence.
The following conversions are supported:
Transcription (seq is DNA, to_material is 'rna')
Reverse transcription (seq is RNA, to_material is 'dna')
Translation (seq is RNA, to_material is 'peptide')
:param seq: DNA or RNA sequence.
:ty... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/reaction/utils.py#L6-L70 |
klavinslab/coral | coral/sequence/_nucleicacid.py | NucleicAcid.gc | def gc(self):
'''Find the frequency of G and C in the current sequence.'''
gc = len([base for base in self.seq if base == 'C' or base == 'G'])
return float(gc) / len(self) | python | def gc(self):
'''Find the frequency of G and C in the current sequence.'''
gc = len([base for base in self.seq if base == 'C' or base == 'G'])
return float(gc) / len(self) | Find the frequency of G and C in the current sequence. | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_nucleicacid.py#L58-L61 |
klavinslab/coral | coral/sequence/_nucleicacid.py | NucleicAcid.is_rotation | def is_rotation(self, other):
'''Determine whether two sequences are the same, just at different
rotations.
:param other: The sequence to check for rotational equality.
:type other: coral.sequence._sequence.Sequence
'''
if len(self) != len(other):
return Fal... | python | def is_rotation(self, other):
'''Determine whether two sequences are the same, just at different
rotations.
:param other: The sequence to check for rotational equality.
:type other: coral.sequence._sequence.Sequence
'''
if len(self) != len(other):
return Fal... | Determine whether two sequences are the same, just at different
rotations.
:param other: The sequence to check for rotational equality.
:type other: coral.sequence._sequence.Sequence | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_nucleicacid.py#L78-L93 |
klavinslab/coral | coral/sequence/_nucleicacid.py | NucleicAcid.linearize | def linearize(self, index=0):
'''Linearize the Sequence at an index.
:param index: index at which to linearize.
:type index: int
:returns: A linearized version of the current sequence.
:rtype: coral.sequence._sequence.Sequence
:raises: ValueError if the input is a linear... | python | def linearize(self, index=0):
'''Linearize the Sequence at an index.
:param index: index at which to linearize.
:type index: int
:returns: A linearized version of the current sequence.
:rtype: coral.sequence._sequence.Sequence
:raises: ValueError if the input is a linear... | Linearize the Sequence at an index.
:param index: index at which to linearize.
:type index: int
:returns: A linearized version of the current sequence.
:rtype: coral.sequence._sequence.Sequence
:raises: ValueError if the input is a linear sequence. | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_nucleicacid.py#L95-L113 |
klavinslab/coral | coral/sequence/_nucleicacid.py | NucleicAcid.locate | def locate(self, pattern):
'''Find sequences matching a pattern.
:param pattern: Sequence for which to find matches.
:type pattern: str
:returns: Indices of pattern matches.
:rtype: list of ints
'''
if self.circular:
if len(pattern) >= 2 * len(self):... | python | def locate(self, pattern):
'''Find sequences matching a pattern.
:param pattern: Sequence for which to find matches.
:type pattern: str
:returns: Indices of pattern matches.
:rtype: list of ints
'''
if self.circular:
if len(pattern) >= 2 * len(self):... | Find sequences matching a pattern.
:param pattern: Sequence for which to find matches.
:type pattern: str
:returns: Indices of pattern matches.
:rtype: list of ints | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_nucleicacid.py#L115-L131 |
klavinslab/coral | coral/sequence/_nucleicacid.py | NucleicAcid.mw | def mw(self):
'''Calculate the molecular weight.
:returns: The molecular weight of the current sequence in amu.
:rtype: float
'''
counter = collections.Counter(self.seq.lower())
mw_a = counter['a'] * 313.2
mw_t = counter['t'] * 304.2
mw_g = counter['g'] ... | python | def mw(self):
'''Calculate the molecular weight.
:returns: The molecular weight of the current sequence in amu.
:rtype: float
'''
counter = collections.Counter(self.seq.lower())
mw_a = counter['a'] * 313.2
mw_t = counter['t'] * 304.2
mw_g = counter['g'] ... | Calculate the molecular weight.
:returns: The molecular weight of the current sequence in amu.
:rtype: float | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_nucleicacid.py#L133-L150 |
klavinslab/coral | coral/sequence/_nucleicacid.py | NucleicAcid.rotate | def rotate(self, n):
'''Rotate Sequence by n bases.
:param n: Number of bases to rotate.
:type n: int
:returns: The current sequence reoriented at `index`.
:rtype: coral.sequence._sequence.Sequence
:raises: ValueError if applied to linear sequence or `index` is
... | python | def rotate(self, n):
'''Rotate Sequence by n bases.
:param n: Number of bases to rotate.
:type n: int
:returns: The current sequence reoriented at `index`.
:rtype: coral.sequence._sequence.Sequence
:raises: ValueError if applied to linear sequence or `index` is
... | Rotate Sequence by n bases.
:param n: Number of bases to rotate.
:type n: int
:returns: The current sequence reoriented at `index`.
:rtype: coral.sequence._sequence.Sequence
:raises: ValueError if applied to linear sequence or `index` is
negative. | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/sequence/_nucleicacid.py#L152-L167 |
klavinslab/coral | coral/reaction/_resect.py | five_resect | def five_resect(dna, n_bases):
'''Remove bases from 5' end of top strand.
:param dna: Sequence to resect.
:type dna: coral.DNA
:param n_bases: Number of bases cut back.
:type n_bases: int
:returns: DNA sequence resected at the 5' end by n_bases.
:rtype: coral.DNA
'''
new_instance =... | python | def five_resect(dna, n_bases):
'''Remove bases from 5' end of top strand.
:param dna: Sequence to resect.
:type dna: coral.DNA
:param n_bases: Number of bases cut back.
:type n_bases: int
:returns: DNA sequence resected at the 5' end by n_bases.
:rtype: coral.DNA
'''
new_instance =... | Remove bases from 5' end of top strand.
:param dna: Sequence to resect.
:type dna: coral.DNA
:param n_bases: Number of bases cut back.
:type n_bases: int
:returns: DNA sequence resected at the 5' end by n_bases.
:rtype: coral.DNA | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/reaction/_resect.py#L5-L24 |
klavinslab/coral | coral/reaction/_resect.py | _remove_end_gaps | def _remove_end_gaps(sequence):
'''Removes double-stranded gaps from ends of the sequence.
:returns: The current sequence with terminal double-strand gaps ('-')
removed.
:rtype: coral.DNA
'''
# Count terminal blank sequences
def count_end_gaps(seq):
gap = coral.DNA('-')
... | python | def _remove_end_gaps(sequence):
'''Removes double-stranded gaps from ends of the sequence.
:returns: The current sequence with terminal double-strand gaps ('-')
removed.
:rtype: coral.DNA
'''
# Count terminal blank sequences
def count_end_gaps(seq):
gap = coral.DNA('-')
... | Removes double-stranded gaps from ends of the sequence.
:returns: The current sequence with terminal double-strand gaps ('-')
removed.
:rtype: coral.DNA | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/reaction/_resect.py#L49-L78 |
klavinslab/coral | coral/analysis/_sequencing/needle.py | needle | def needle(reference, query, gap_open=-15, gap_extend=0,
matrix=submat.DNA_SIMPLE):
'''Do a Needleman-Wunsch alignment.
:param reference: Reference sequence.
:type reference: coral.DNA
:param query: Sequence to align against the reference.
:type query: coral.DNA
:param gapopen: Penal... | python | def needle(reference, query, gap_open=-15, gap_extend=0,
matrix=submat.DNA_SIMPLE):
'''Do a Needleman-Wunsch alignment.
:param reference: Reference sequence.
:type reference: coral.DNA
:param query: Sequence to align against the reference.
:type query: coral.DNA
:param gapopen: Penal... | Do a Needleman-Wunsch alignment.
:param reference: Reference sequence.
:type reference: coral.DNA
:param query: Sequence to align against the reference.
:type query: coral.DNA
:param gapopen: Penalty for opening a gap.
:type gapopen: float
:param gapextend: Penalty for extending a gap.
... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequencing/needle.py#L16-L48 |
klavinslab/coral | coral/analysis/_sequencing/needle.py | needle_msa | def needle_msa(reference, results, gap_open=-15, gap_extend=0,
matrix=submat.DNA_SIMPLE):
'''Create a multiple sequence alignment based on aligning every result
sequence against the reference, then inserting gaps until every aligned
reference is identical
'''
gap = '-'
# Convert ... | python | def needle_msa(reference, results, gap_open=-15, gap_extend=0,
matrix=submat.DNA_SIMPLE):
'''Create a multiple sequence alignment based on aligning every result
sequence against the reference, then inserting gaps until every aligned
reference is identical
'''
gap = '-'
# Convert ... | Create a multiple sequence alignment based on aligning every result
sequence against the reference, then inserting gaps until every aligned
reference is identical | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequencing/needle.py#L58-L113 |
klavinslab/coral | coral/analysis/_sequencing/needle.py | needle_multi | def needle_multi(references, queries, gap_open=-15, gap_extend=0,
matrix=submat.DNA_SIMPLE):
'''Batch process of sequencing split over several cores. Acts just like
needle but sequence inputs are lists.
:param references: References sequence.
:type references: coral.DNA list
:param... | python | def needle_multi(references, queries, gap_open=-15, gap_extend=0,
matrix=submat.DNA_SIMPLE):
'''Batch process of sequencing split over several cores. Acts just like
needle but sequence inputs are lists.
:param references: References sequence.
:type references: coral.DNA list
:param... | Batch process of sequencing split over several cores. Acts just like
needle but sequence inputs are lists.
:param references: References sequence.
:type references: coral.DNA list
:param queries: Sequences to align against the reference.
:type queries: coral.DNA list
:param gap_open: Penalty fo... | https://github.com/klavinslab/coral/blob/17f59591211562a59a051f474cd6cecba4829df9/coral/analysis/_sequencing/needle.py#L116-L147 |
WoLpH/python-utils | python_utils/import_.py | import_global | def import_global(
name, modules=None, exceptions=DummyException, locals_=None,
globals_=None, level=-1):
'''Import the requested items into the global scope
WARNING! this method _will_ overwrite your global scope
If you have a variable named "path" and you call import_global('sys')
it ... | python | def import_global(
name, modules=None, exceptions=DummyException, locals_=None,
globals_=None, level=-1):
'''Import the requested items into the global scope
WARNING! this method _will_ overwrite your global scope
If you have a variable named "path" and you call import_global('sys')
it ... | Import the requested items into the global scope
WARNING! this method _will_ overwrite your global scope
If you have a variable named "path" and you call import_global('sys')
it will be overwritten with sys.path
Args:
name (str): the name of the module to import, e.g. sys
modules (str)... | https://github.com/WoLpH/python-utils/blob/6bbe13bab33bd9965b0edd379f26261b31a3e427/python_utils/import_.py#L6-L78 |
WoLpH/python-utils | python_utils/formatters.py | camel_to_underscore | def camel_to_underscore(name):
'''Convert camel case style naming to underscore style naming
If there are existing underscores they will be collapsed with the
to-be-added underscores. Multiple consecutive capital letters will not be
split except for the last one.
>>> camel_to_underscore('SpamEggsA... | python | def camel_to_underscore(name):
'''Convert camel case style naming to underscore style naming
If there are existing underscores they will be collapsed with the
to-be-added underscores. Multiple consecutive capital letters will not be
split except for the last one.
>>> camel_to_underscore('SpamEggsA... | Convert camel case style naming to underscore style naming
If there are existing underscores they will be collapsed with the
to-be-added underscores. Multiple consecutive capital letters will not be
split except for the last one.
>>> camel_to_underscore('SpamEggsAndBacon')
'spam_eggs_and_bacon'
... | https://github.com/WoLpH/python-utils/blob/6bbe13bab33bd9965b0edd379f26261b31a3e427/python_utils/formatters.py#L4-L39 |
WoLpH/python-utils | python_utils/formatters.py | timesince | def timesince(dt, default='just now'):
'''
Returns string representing 'time since' e.g.
3 days ago, 5 hours ago etc.
>>> now = datetime.datetime.now()
>>> timesince(now)
'just now'
>>> timesince(now - datetime.timedelta(seconds=1))
'1 second ago'
>>> timesince(now - datetime.timede... | python | def timesince(dt, default='just now'):
'''
Returns string representing 'time since' e.g.
3 days ago, 5 hours ago etc.
>>> now = datetime.datetime.now()
>>> timesince(now)
'just now'
>>> timesince(now - datetime.timedelta(seconds=1))
'1 second ago'
>>> timesince(now - datetime.timede... | Returns string representing 'time since' e.g.
3 days ago, 5 hours ago etc.
>>> now = datetime.datetime.now()
>>> timesince(now)
'just now'
>>> timesince(now - datetime.timedelta(seconds=1))
'1 second ago'
>>> timesince(now - datetime.timedelta(seconds=2))
'2 seconds ago'
>>> timesin... | https://github.com/WoLpH/python-utils/blob/6bbe13bab33bd9965b0edd379f26261b31a3e427/python_utils/formatters.py#L42-L112 |
WoLpH/python-utils | python_utils/time.py | timedelta_to_seconds | def timedelta_to_seconds(delta):
'''Convert a timedelta to seconds with the microseconds as fraction
Note that this method has become largely obsolete with the
`timedelta.total_seconds()` method introduced in Python 2.7.
>>> from datetime import timedelta
>>> '%d' % timedelta_to_seconds(timedelta(... | python | def timedelta_to_seconds(delta):
'''Convert a timedelta to seconds with the microseconds as fraction
Note that this method has become largely obsolete with the
`timedelta.total_seconds()` method introduced in Python 2.7.
>>> from datetime import timedelta
>>> '%d' % timedelta_to_seconds(timedelta(... | Convert a timedelta to seconds with the microseconds as fraction
Note that this method has become largely obsolete with the
`timedelta.total_seconds()` method introduced in Python 2.7.
>>> from datetime import timedelta
>>> '%d' % timedelta_to_seconds(timedelta(days=1))
'86400'
>>> '%d' % time... | https://github.com/WoLpH/python-utils/blob/6bbe13bab33bd9965b0edd379f26261b31a3e427/python_utils/time.py#L10-L33 |
WoLpH/python-utils | python_utils/time.py | format_time | def format_time(timestamp, precision=datetime.timedelta(seconds=1)):
'''Formats timedelta/datetime/seconds
>>> format_time('1')
'0:00:01'
>>> format_time(1.234)
'0:00:01'
>>> format_time(1)
'0:00:01'
>>> format_time(datetime.datetime(2000, 1, 2, 3, 4, 5, 6))
'2000-01-02 03:04:05'
... | python | def format_time(timestamp, precision=datetime.timedelta(seconds=1)):
'''Formats timedelta/datetime/seconds
>>> format_time('1')
'0:00:01'
>>> format_time(1.234)
'0:00:01'
>>> format_time(1)
'0:00:01'
>>> format_time(datetime.datetime(2000, 1, 2, 3, 4, 5, 6))
'2000-01-02 03:04:05'
... | Formats timedelta/datetime/seconds
>>> format_time('1')
'0:00:01'
>>> format_time(1.234)
'0:00:01'
>>> format_time(1)
'0:00:01'
>>> format_time(datetime.datetime(2000, 1, 2, 3, 4, 5, 6))
'2000-01-02 03:04:05'
>>> format_time(datetime.date(2000, 1, 2))
'2000-01-02'
>>> format... | https://github.com/WoLpH/python-utils/blob/6bbe13bab33bd9965b0edd379f26261b31a3e427/python_utils/time.py#L36-L97 |
WoLpH/python-utils | python_utils/terminal.py | get_terminal_size | def get_terminal_size(): # pragma: no cover
'''Get the current size of your terminal
Multiple returns are not always a good idea, but in this case it greatly
simplifies the code so I believe it's justified. It's not the prettiest
function but that's never really possible with cross-platform code.
... | python | def get_terminal_size(): # pragma: no cover
'''Get the current size of your terminal
Multiple returns are not always a good idea, but in this case it greatly
simplifies the code so I believe it's justified. It's not the prettiest
function but that's never really possible with cross-platform code.
... | Get the current size of your terminal
Multiple returns are not always a good idea, but in this case it greatly
simplifies the code so I believe it's justified. It's not the prettiest
function but that's never really possible with cross-platform code.
Returns:
width, height: Two integers contai... | https://github.com/WoLpH/python-utils/blob/6bbe13bab33bd9965b0edd379f26261b31a3e427/python_utils/terminal.py#L4-L78 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.AsyncSearchUsers | def AsyncSearchUsers(self, Target):
"""Asynchronously searches for Skype users.
:Parameters:
Target : unicode
Search target (name or email address).
:return: A search identifier. It will be passed along with the results to the
`SkypeEvents.AsyncSearchUser... | python | def AsyncSearchUsers(self, Target):
"""Asynchronously searches for Skype users.
:Parameters:
Target : unicode
Search target (name or email address).
:return: A search identifier. It will be passed along with the results to the
`SkypeEvents.AsyncSearchUser... | Asynchronously searches for Skype users.
:Parameters:
Target : unicode
Search target (name or email address).
:return: A search identifier. It will be passed along with the results to the
`SkypeEvents.AsyncSearchUsersFinished` event after the search is completed.... | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L376-L394 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.Attach | def Attach(self, Protocol=5, Wait=True):
"""Establishes a connection to Skype.
:Parameters:
Protocol : int
Minimal Skype protocol version.
Wait : bool
If set to False, blocks forever until the connection is established. Otherwise, timeouts
after t... | python | def Attach(self, Protocol=5, Wait=True):
"""Establishes a connection to Skype.
:Parameters:
Protocol : int
Minimal Skype protocol version.
Wait : bool
If set to False, blocks forever until the connection is established. Otherwise, timeouts
after t... | Establishes a connection to Skype.
:Parameters:
Protocol : int
Minimal Skype protocol version.
Wait : bool
If set to False, blocks forever until the connection is established. Otherwise, timeouts
after the `Timeout`. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L396-L411 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.Call | def Call(self, Id=0):
"""Queries a call object.
:Parameters:
Id : int
Call identifier.
:return: Call object.
:rtype: `call.Call`
"""
o = Call(self, Id)
o.Status # Test if such a call exists.
return o | python | def Call(self, Id=0):
"""Queries a call object.
:Parameters:
Id : int
Call identifier.
:return: Call object.
:rtype: `call.Call`
"""
o = Call(self, Id)
o.Status # Test if such a call exists.
return o | Queries a call object.
:Parameters:
Id : int
Call identifier.
:return: Call object.
:rtype: `call.Call` | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L413-L425 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.ChangeUserStatus | def ChangeUserStatus(self, Status):
"""Changes the online status for the current user.
:Parameters:
Status : `enums`.cus*
New online status for the user.
:note: This function waits until the online status changes. Alternatively, use the
`CurrentUserStatus` ... | python | def ChangeUserStatus(self, Status):
"""Changes the online status for the current user.
:Parameters:
Status : `enums`.cus*
New online status for the user.
:note: This function waits until the online status changes. Alternatively, use the
`CurrentUserStatus` ... | Changes the online status for the current user.
:Parameters:
Status : `enums`.cus*
New online status for the user.
:note: This function waits until the online status changes. Alternatively, use the
`CurrentUserStatus` property to perform an immediate change of stat... | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L443-L461 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.Chat | def Chat(self, Name=''):
"""Queries a chat object.
:Parameters:
Name : str
Chat name.
:return: A chat object.
:rtype: `chat.Chat`
"""
o = Chat(self, Name)
o.Status # Tests if such a chat really exists.
return o | python | def Chat(self, Name=''):
"""Queries a chat object.
:Parameters:
Name : str
Chat name.
:return: A chat object.
:rtype: `chat.Chat`
"""
o = Chat(self, Name)
o.Status # Tests if such a chat really exists.
return o | Queries a chat object.
:Parameters:
Name : str
Chat name.
:return: A chat object.
:rtype: `chat.Chat` | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L463-L475 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.ClearCallHistory | def ClearCallHistory(self, Username='ALL', Type=chsAllCalls):
"""Clears the call history.
:Parameters:
Username : str
Skypename of the user. A special value of 'ALL' means that entries of all users should
be removed.
Type : `enums`.clt*
Call type.... | python | def ClearCallHistory(self, Username='ALL', Type=chsAllCalls):
"""Clears the call history.
:Parameters:
Username : str
Skypename of the user. A special value of 'ALL' means that entries of all users should
be removed.
Type : `enums`.clt*
Call type.... | Clears the call history.
:Parameters:
Username : str
Skypename of the user. A special value of 'ALL' means that entries of all users should
be removed.
Type : `enums`.clt*
Call type. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L477-L488 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.Command | def Command(self, Command, Reply=u'', Block=False, Timeout=30000, Id=-1):
"""Creates an API command object.
:Parameters:
Command : unicode
Command string.
Reply : unicode
Expected reply. By default any reply is accepted (except errors which raise an
... | python | def Command(self, Command, Reply=u'', Block=False, Timeout=30000, Id=-1):
"""Creates an API command object.
:Parameters:
Command : unicode
Command string.
Reply : unicode
Expected reply. By default any reply is accepted (except errors which raise an
... | Creates an API command object.
:Parameters:
Command : unicode
Command string.
Reply : unicode
Expected reply. By default any reply is accepted (except errors which raise an
`SkypeError` exception).
Block : bool
If set to True, `SendC... | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L501-L526 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.Conference | def Conference(self, Id=0):
"""Queries a call conference object.
:Parameters:
Id : int
Conference Id.
:return: A conference object.
:rtype: `Conference`
"""
o = Conference(self, Id)
if Id <= 0 or not o.Calls:
raise SkypeError(0,... | python | def Conference(self, Id=0):
"""Queries a call conference object.
:Parameters:
Id : int
Conference Id.
:return: A conference object.
:rtype: `Conference`
"""
o = Conference(self, Id)
if Id <= 0 or not o.Calls:
raise SkypeError(0,... | Queries a call conference object.
:Parameters:
Id : int
Conference Id.
:return: A conference object.
:rtype: `Conference` | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L528-L541 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.CreateChatWith | def CreateChatWith(self, *Usernames):
"""Creates a chat with one or more users.
:Parameters:
Usernames : str
One or more Skypenames of the users.
:return: A chat object
:rtype: `Chat`
:see: `Chat.AddMembers`
"""
return Chat(self, chop(self... | python | def CreateChatWith(self, *Usernames):
"""Creates a chat with one or more users.
:Parameters:
Usernames : str
One or more Skypenames of the users.
:return: A chat object
:rtype: `Chat`
:see: `Chat.AddMembers`
"""
return Chat(self, chop(self... | Creates a chat with one or more users.
:Parameters:
Usernames : str
One or more Skypenames of the users.
:return: A chat object
:rtype: `Chat`
:see: `Chat.AddMembers` | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L555-L567 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.CreateGroup | def CreateGroup(self, GroupName):
"""Creates a custom contact group.
:Parameters:
GroupName : unicode
Group name.
:return: A group object.
:rtype: `Group`
:see: `DeleteGroup`
"""
groups = self.CustomGroups
self._DoCommand('CREATE G... | python | def CreateGroup(self, GroupName):
"""Creates a custom contact group.
:Parameters:
GroupName : unicode
Group name.
:return: A group object.
:rtype: `Group`
:see: `DeleteGroup`
"""
groups = self.CustomGroups
self._DoCommand('CREATE G... | Creates a custom contact group.
:Parameters:
GroupName : unicode
Group name.
:return: A group object.
:rtype: `Group`
:see: `DeleteGroup` | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L569-L586 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.CreateSms | def CreateSms(self, MessageType, *TargetNumbers):
"""Creates an SMS message.
:Parameters:
MessageType : `enums`.smsMessageType*
Message type.
TargetNumbers : str
One or more target SMS numbers.
:return: An sms message object.
:rtype: `SmsMess... | python | def CreateSms(self, MessageType, *TargetNumbers):
"""Creates an SMS message.
:Parameters:
MessageType : `enums`.smsMessageType*
Message type.
TargetNumbers : str
One or more target SMS numbers.
:return: An sms message object.
:rtype: `SmsMess... | Creates an SMS message.
:Parameters:
MessageType : `enums`.smsMessageType*
Message type.
TargetNumbers : str
One or more target SMS numbers.
:return: An sms message object.
:rtype: `SmsMessage` | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L588-L600 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.Greeting | def Greeting(self, Username=''):
"""Queries the greeting used as voicemail.
:Parameters:
Username : str
Skypename of the user.
:return: A voicemail object.
:rtype: `Voicemail`
"""
for v in self.Voicemails:
if Username and v.PartnerHandl... | python | def Greeting(self, Username=''):
"""Queries the greeting used as voicemail.
:Parameters:
Username : str
Skypename of the user.
:return: A voicemail object.
:rtype: `Voicemail`
"""
for v in self.Voicemails:
if Username and v.PartnerHandl... | Queries the greeting used as voicemail.
:Parameters:
Username : str
Skypename of the user.
:return: A voicemail object.
:rtype: `Voicemail` | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L638-L652 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.Message | def Message(self, Id=0):
"""Queries a chat message object.
:Parameters:
Id : int
Message Id.
:return: A chat message object.
:rtype: `ChatMessage`
"""
o = ChatMessage(self, Id)
o.Status # Test if such an id is known.
return o | python | def Message(self, Id=0):
"""Queries a chat message object.
:Parameters:
Id : int
Message Id.
:return: A chat message object.
:rtype: `ChatMessage`
"""
o = ChatMessage(self, Id)
o.Status # Test if such an id is known.
return o | Queries a chat message object.
:Parameters:
Id : int
Message Id.
:return: A chat message object.
:rtype: `ChatMessage` | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L654-L666 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.PlaceCall | def PlaceCall(self, *Targets):
"""Places a call to a single user or creates a conference call.
:Parameters:
Targets : str
One or more call targets. If multiple targets are specified, a conference call is
created. The call target can be a Skypename, phone number, or spe... | python | def PlaceCall(self, *Targets):
"""Places a call to a single user or creates a conference call.
:Parameters:
Targets : str
One or more call targets. If multiple targets are specified, a conference call is
created. The call target can be a Skypename, phone number, or spe... | Places a call to a single user or creates a conference call.
:Parameters:
Targets : str
One or more call targets. If multiple targets are specified, a conference call is
created. The call target can be a Skypename, phone number, or speed dial code.
:return: A call obj... | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L680-L701 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.Property | def Property(self, ObjectType, ObjectId, PropName, Set=None):
"""Queries/sets the properties of an object.
:Parameters:
ObjectType : str
Object type ('USER', 'CALL', 'CHAT', 'CHATMESSAGE', ...).
ObjectId : str
Object Id, depends on the object type.
... | python | def Property(self, ObjectType, ObjectId, PropName, Set=None):
"""Queries/sets the properties of an object.
:Parameters:
ObjectType : str
Object type ('USER', 'CALL', 'CHAT', 'CHATMESSAGE', ...).
ObjectId : str
Object Id, depends on the object type.
... | Queries/sets the properties of an object.
:Parameters:
ObjectType : str
Object type ('USER', 'CALL', 'CHAT', 'CHATMESSAGE', ...).
ObjectId : str
Object Id, depends on the object type.
PropName : str
Name of the property to access.
Set ... | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L731-L747 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.SendCommand | def SendCommand(self, Command):
"""Sends an API command.
:Parameters:
Command : `Command`
Command to send. Use `Command` method to create a command.
"""
try:
self._Api.send_command(Command)
except SkypeAPIError:
self.ResetCache()
... | python | def SendCommand(self, Command):
"""Sends an API command.
:Parameters:
Command : `Command`
Command to send. Use `Command` method to create a command.
"""
try:
self._Api.send_command(Command)
except SkypeAPIError:
self.ResetCache()
... | Sends an API command.
:Parameters:
Command : `Command`
Command to send. Use `Command` method to create a command. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L770-L781 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.SendSms | def SendSms(self, *TargetNumbers, **Properties):
"""Creates and sends an SMS message.
:Parameters:
TargetNumbers : str
One or more target SMS numbers.
Properties
Message properties. Properties available are same as `SmsMessage` object properties.
:re... | python | def SendSms(self, *TargetNumbers, **Properties):
"""Creates and sends an SMS message.
:Parameters:
TargetNumbers : str
One or more target SMS numbers.
Properties
Message properties. Properties available are same as `SmsMessage` object properties.
:re... | Creates and sends an SMS message.
:Parameters:
TargetNumbers : str
One or more target SMS numbers.
Properties
Message properties. Properties available are same as `SmsMessage` object properties.
:return: An sms message object. The message is already sent at ... | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L797-L816 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.SendVoicemail | def SendVoicemail(self, Username):
"""Sends a voicemail to a specified user.
:Parameters:
Username : str
Skypename of the user.
:note: Should return a `Voicemail` object. This is not implemented yet.
"""
if self._Api.protocol >= 6:
self._DoComm... | python | def SendVoicemail(self, Username):
"""Sends a voicemail to a specified user.
:Parameters:
Username : str
Skypename of the user.
:note: Should return a `Voicemail` object. This is not implemented yet.
"""
if self._Api.protocol >= 6:
self._DoComm... | Sends a voicemail to a specified user.
:Parameters:
Username : str
Skypename of the user.
:note: Should return a `Voicemail` object. This is not implemented yet. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L818-L830 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.User | def User(self, Username=''):
"""Queries a user object.
:Parameters:
Username : str
Skypename of the user.
:return: A user object.
:rtype: `user.User`
"""
if not Username:
Username = self.CurrentUserHandle
o = User(self, Username... | python | def User(self, Username=''):
"""Queries a user object.
:Parameters:
Username : str
Skypename of the user.
:return: A user object.
:rtype: `user.User`
"""
if not Username:
Username = self.CurrentUserHandle
o = User(self, Username... | Queries a user object.
:Parameters:
Username : str
Skypename of the user.
:return: A user object.
:rtype: `user.User` | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L832-L846 |
Skype4Py/Skype4Py | Skype4Py/skype.py | Skype.Voicemail | def Voicemail(self, Id):
"""Queries the voicemail object.
:Parameters:
Id : int
Voicemail Id.
:return: A voicemail object.
:rtype: `Voicemail`
"""
o = Voicemail(self, Id)
o.Type # Test if such a voicemail exists.
return o | python | def Voicemail(self, Id):
"""Queries the voicemail object.
:Parameters:
Id : int
Voicemail Id.
:return: A voicemail object.
:rtype: `Voicemail`
"""
o = Voicemail(self, Id)
o.Type # Test if such a voicemail exists.
return o | Queries the voicemail object.
:Parameters:
Id : int
Voicemail Id.
:return: A voicemail object.
:rtype: `Voicemail` | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/skype.py#L862-L874 |
Skype4Py/Skype4Py | Skype4Py/application.py | Application.Connect | def Connect(self, Username, WaitConnected=False):
"""Connects application to user.
:Parameters:
Username : str
Name of the user to connect to.
WaitConnected : bool
If True, causes the method to wait until the connection is established.
:return: If ``... | python | def Connect(self, Username, WaitConnected=False):
"""Connects application to user.
:Parameters:
Username : str
Name of the user to connect to.
WaitConnected : bool
If True, causes the method to wait until the connection is established.
:return: If ``... | Connects application to user.
:Parameters:
Username : str
Name of the user to connect to.
WaitConnected : bool
If True, causes the method to wait until the connection is established.
:return: If ``WaitConnected`` is True, returns the stream which can be used... | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/application.py#L36-L63 |
Skype4Py/Skype4Py | Skype4Py/application.py | Application.SendDatagram | def SendDatagram(self, Text, Streams=None):
"""Sends datagram to application streams.
:Parameters:
Text : unicode
Text to send.
Streams : sequence of `ApplicationStream`
Streams to send the datagram to or None if all currently connected streams should be
... | python | def SendDatagram(self, Text, Streams=None):
"""Sends datagram to application streams.
:Parameters:
Text : unicode
Text to send.
Streams : sequence of `ApplicationStream`
Streams to send the datagram to or None if all currently connected streams should be
... | Sends datagram to application streams.
:Parameters:
Text : unicode
Text to send.
Streams : sequence of `ApplicationStream`
Streams to send the datagram to or None if all currently connected streams should be
used. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/application.py#L75-L88 |
Skype4Py/Skype4Py | Skype4Py/application.py | ApplicationStream.SendDatagram | def SendDatagram(self, Text):
"""Sends datagram to stream.
:Parameters:
Text : unicode
Datagram to send.
"""
self.Application._Alter('DATAGRAM', '%s %s' % (self.Handle, tounicode(Text))) | python | def SendDatagram(self, Text):
"""Sends datagram to stream.
:Parameters:
Text : unicode
Datagram to send.
"""
self.Application._Alter('DATAGRAM', '%s %s' % (self.Handle, tounicode(Text))) | Sends datagram to stream.
:Parameters:
Text : unicode
Datagram to send. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/application.py#L173-L180 |
Skype4Py/Skype4Py | Skype4Py/application.py | ApplicationStream.Write | def Write(self, Text):
"""Writes data to stream.
:Parameters:
Text : unicode
Data to send.
"""
self.Application._Alter('WRITE', '%s %s' % (self.Handle, tounicode(Text))) | python | def Write(self, Text):
"""Writes data to stream.
:Parameters:
Text : unicode
Data to send.
"""
self.Application._Alter('WRITE', '%s %s' % (self.Handle, tounicode(Text))) | Writes data to stream.
:Parameters:
Text : unicode
Data to send. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/application.py#L182-L189 |
Skype4Py/Skype4Py | Skype4Py/client.py | Client.CreateEvent | def CreateEvent(self, EventId, Caption, Hint):
"""Creates a custom event displayed in Skype client's events pane.
:Parameters:
EventId : unicode
Unique identifier for the event.
Caption : unicode
Caption text.
Hint : unicode
Hint text. S... | python | def CreateEvent(self, EventId, Caption, Hint):
"""Creates a custom event displayed in Skype client's events pane.
:Parameters:
EventId : unicode
Unique identifier for the event.
Caption : unicode
Caption text.
Hint : unicode
Hint text. S... | Creates a custom event displayed in Skype client's events pane.
:Parameters:
EventId : unicode
Unique identifier for the event.
Caption : unicode
Caption text.
Hint : unicode
Hint text. Shown when mouse hoovers over the event.
:return: ... | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/client.py#L44-L60 |
Skype4Py/Skype4Py | Skype4Py/client.py | Client.CreateMenuItem | def CreateMenuItem(self, MenuItemId, PluginContext, CaptionText, HintText=u'', IconPath='', Enabled=True,
ContactType=pluginContactTypeAll, MultipleContacts=False):
"""Creates custom menu item in Skype client's "Do More" menus.
:Parameters:
MenuItemId : unicode
... | python | def CreateMenuItem(self, MenuItemId, PluginContext, CaptionText, HintText=u'', IconPath='', Enabled=True,
ContactType=pluginContactTypeAll, MultipleContacts=False):
"""Creates custom menu item in Skype client's "Do More" menus.
:Parameters:
MenuItemId : unicode
... | Creates custom menu item in Skype client's "Do More" menus.
:Parameters:
MenuItemId : unicode
Unique identifier for the menu item.
PluginContext : `enums`.pluginContext*
Menu item context. Allows to choose in which client windows will the menu item appear.
... | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/client.py#L62-L99 |
Skype4Py/Skype4Py | Skype4Py/client.py | Client.Focus | def Focus(self):
"""Brings the client window into focus.
"""
self._Skype._Api.allow_focus(self._Skype.Timeout)
self._Skype._DoCommand('FOCUS') | python | def Focus(self):
"""Brings the client window into focus.
"""
self._Skype._Api.allow_focus(self._Skype.Timeout)
self._Skype._DoCommand('FOCUS') | Brings the client window into focus. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/client.py#L101-L105 |
Skype4Py/Skype4Py | Skype4Py/client.py | Client.OpenDialog | def OpenDialog(self, Name, *Params):
"""Open dialog. Use this method to open dialogs added in newer Skype versions if there is no
dedicated method in Skype4Py.
:Parameters:
Name : str
Dialog name.
Params : unicode
One or more optional parameters.
... | python | def OpenDialog(self, Name, *Params):
"""Open dialog. Use this method to open dialogs added in newer Skype versions if there is no
dedicated method in Skype4Py.
:Parameters:
Name : str
Dialog name.
Params : unicode
One or more optional parameters.
... | Open dialog. Use this method to open dialogs added in newer Skype versions if there is no
dedicated method in Skype4Py.
:Parameters:
Name : str
Dialog name.
Params : unicode
One or more optional parameters. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/client.py#L150-L162 |
Skype4Py/Skype4Py | Skype4Py/client.py | Client.OpenMessageDialog | def OpenMessageDialog(self, Username, Text=u''):
"""Opens "Send an IM Message" dialog.
:Parameters:
Username : str
Message target.
Text : unicode
Message text.
"""
self.OpenDialog('IM', Username, tounicode(Text)) | python | def OpenMessageDialog(self, Username, Text=u''):
"""Opens "Send an IM Message" dialog.
:Parameters:
Username : str
Message target.
Text : unicode
Message text.
"""
self.OpenDialog('IM', Username, tounicode(Text)) | Opens "Send an IM Message" dialog.
:Parameters:
Username : str
Message target.
Text : unicode
Message text. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/client.py#L195-L204 |
Skype4Py/Skype4Py | Skype4Py/client.py | Client.Start | def Start(self, Minimized=False, Nosplash=False):
"""Starts Skype application.
:Parameters:
Minimized : bool
If True, Skype is started minimized in system tray.
Nosplash : bool
If True, no splash screen is displayed upon startup.
"""
self._Sky... | python | def Start(self, Minimized=False, Nosplash=False):
"""Starts Skype application.
:Parameters:
Minimized : bool
If True, Skype is started minimized in system tray.
Nosplash : bool
If True, no splash screen is displayed upon startup.
"""
self._Sky... | Starts Skype application.
:Parameters:
Minimized : bool
If True, Skype is started minimized in system tray.
Nosplash : bool
If True, no splash screen is displayed upon startup. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/client.py#L264-L273 |
Skype4Py/Skype4Py | Skype4Py/api/darwin.py | SkypeAPI.start | def start(self):
"""
Start the thread associated with this API object.
Ensure that the call is made no more than once,
to avoid raising a RuntimeError.
"""
if not self.thread_started:
super(SkypeAPI, self).start()
self.thread_started = True | python | def start(self):
"""
Start the thread associated with this API object.
Ensure that the call is made no more than once,
to avoid raising a RuntimeError.
"""
if not self.thread_started:
super(SkypeAPI, self).start()
self.thread_started = True | Start the thread associated with this API object.
Ensure that the call is made no more than once,
to avoid raising a RuntimeError. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/api/darwin.py#L302-L310 |
Skype4Py/Skype4Py | Skype4Py/api/posix_x11.py | threads_init | def threads_init(gtk=True):
"""Enables multithreading support in Xlib and PyGTK.
See the module docstring for more info.
:Parameters:
gtk : bool
May be set to False to skip the PyGTK module.
"""
# enable X11 multithreading
x11.XInitThreads()
if gtk:
from gtk.gdk im... | python | def threads_init(gtk=True):
"""Enables multithreading support in Xlib and PyGTK.
See the module docstring for more info.
:Parameters:
gtk : bool
May be set to False to skip the PyGTK module.
"""
# enable X11 multithreading
x11.XInitThreads()
if gtk:
from gtk.gdk im... | Enables multithreading support in Xlib and PyGTK.
See the module docstring for more info.
:Parameters:
gtk : bool
May be set to False to skip the PyGTK module. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/api/posix_x11.py#L227-L239 |
Skype4Py/Skype4Py | Skype4Py/api/posix_x11.py | SkypeAPI.get_skype | def get_skype(self):
"""Returns Skype window ID or None if Skype not running."""
skype_inst = x11.XInternAtom(self.disp, '_SKYPE_INSTANCE', True)
if not skype_inst:
return
type_ret = Atom()
format_ret = c_int()
nitems_ret = c_ulong()
bytes_after_ret = ... | python | def get_skype(self):
"""Returns Skype window ID or None if Skype not running."""
skype_inst = x11.XInternAtom(self.disp, '_SKYPE_INSTANCE', True)
if not skype_inst:
return
type_ret = Atom()
format_ret = c_int()
nitems_ret = c_ulong()
bytes_after_ret = ... | Returns Skype window ID or None if Skype not running. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/api/posix_x11.py#L323-L337 |
Skype4Py/Skype4Py | Skype4Py/call.py | Call.Join | def Join(self, Id):
"""Joins with another call to form a conference.
:Parameters:
Id : int
Call Id of the other call to join to the conference.
:return: Conference object.
:rtype: `Conference`
"""
#self._Alter('JOIN_CONFERENCE', Id)
reply =... | python | def Join(self, Id):
"""Joins with another call to form a conference.
:Parameters:
Id : int
Call Id of the other call to join to the conference.
:return: Conference object.
:rtype: `Conference`
"""
#self._Alter('JOIN_CONFERENCE', Id)
reply =... | Joins with another call to form a conference.
:Parameters:
Id : int
Call Id of the other call to join to the conference.
:return: Conference object.
:rtype: `Conference` | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/call.py#L175-L188 |
Skype4Py/Skype4Py | Skype4Py/settings.py | Settings.Avatar | def Avatar(self, Id=1, Set=None):
"""Sets user avatar picture from file.
:Parameters:
Id : int
Optional avatar Id.
Set : str
New avatar file name.
:deprecated: Use `LoadAvatarFromFile` instead.
"""
from warnings import warn
wa... | python | def Avatar(self, Id=1, Set=None):
"""Sets user avatar picture from file.
:Parameters:
Id : int
Optional avatar Id.
Set : str
New avatar file name.
:deprecated: Use `LoadAvatarFromFile` instead.
"""
from warnings import warn
wa... | Sets user avatar picture from file.
:Parameters:
Id : int
Optional avatar Id.
Set : str
New avatar file name.
:deprecated: Use `LoadAvatarFromFile` instead. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/settings.py#L25-L40 |
Skype4Py/Skype4Py | Skype4Py/settings.py | Settings.LoadAvatarFromFile | def LoadAvatarFromFile(self, Filename, AvatarId=1):
"""Loads user avatar picture from file.
:Parameters:
Filename : str
Name of the avatar file.
AvatarId : int
Optional avatar Id.
"""
s = 'AVATAR %s %s' % (AvatarId, path2unicode(Filename))
... | python | def LoadAvatarFromFile(self, Filename, AvatarId=1):
"""Loads user avatar picture from file.
:Parameters:
Filename : str
Name of the avatar file.
AvatarId : int
Optional avatar Id.
"""
s = 'AVATAR %s %s' % (AvatarId, path2unicode(Filename))
... | Loads user avatar picture from file.
:Parameters:
Filename : str
Name of the avatar file.
AvatarId : int
Optional avatar Id. | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/settings.py#L42-L52 |
Skype4Py/Skype4Py | Skype4Py/settings.py | Settings.RingTone | def RingTone(self, Id=1, Set=None):
"""Returns/sets a ringtone.
:Parameters:
Id : int
Ringtone Id
Set : str
Path to new ringtone or None if the current path should be queried.
:return: Current path if Set=None, None otherwise.
:rtype: str or ... | python | def RingTone(self, Id=1, Set=None):
"""Returns/sets a ringtone.
:Parameters:
Id : int
Ringtone Id
Set : str
Path to new ringtone or None if the current path should be queried.
:return: Current path if Set=None, None otherwise.
:rtype: str or ... | Returns/sets a ringtone.
:Parameters:
Id : int
Ringtone Id
Set : str
Path to new ringtone or None if the current path should be queried.
:return: Current path if Set=None, None otherwise.
:rtype: str or None | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/settings.py#L59-L73 |
Skype4Py/Skype4Py | Skype4Py/settings.py | Settings.RingToneStatus | def RingToneStatus(self, Id=1, Set=None):
"""Enables/disables a ringtone.
:Parameters:
Id : int
Ringtone Id
Set : bool
True/False if the ringtone should be enabled/disabled or None if the current status
should be queried.
:return: Current... | python | def RingToneStatus(self, Id=1, Set=None):
"""Enables/disables a ringtone.
:Parameters:
Id : int
Ringtone Id
Set : bool
True/False if the ringtone should be enabled/disabled or None if the current status
should be queried.
:return: Current... | Enables/disables a ringtone.
:Parameters:
Id : int
Ringtone Id
Set : bool
True/False if the ringtone should be enabled/disabled or None if the current status
should be queried.
:return: Current status if Set=None, None otherwise.
:rtype: ... | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/settings.py#L75-L90 |
Skype4Py/Skype4Py | Skype4Py/settings.py | Settings.SaveAvatarToFile | def SaveAvatarToFile(self, Filename, AvatarId=1):
"""Saves user avatar picture to file.
:Parameters:
Filename : str
Destination path.
AvatarId : int
Avatar Id
"""
s = 'AVATAR %s %s' % (AvatarId, path2unicode(Filename))
self._Skype._DoC... | python | def SaveAvatarToFile(self, Filename, AvatarId=1):
"""Saves user avatar picture to file.
:Parameters:
Filename : str
Destination path.
AvatarId : int
Avatar Id
"""
s = 'AVATAR %s %s' % (AvatarId, path2unicode(Filename))
self._Skype._DoC... | Saves user avatar picture to file.
:Parameters:
Filename : str
Destination path.
AvatarId : int
Avatar Id | https://github.com/Skype4Py/Skype4Py/blob/c48d83f7034109fe46315d45a066126002c6e0d4/Skype4Py/settings.py#L92-L102 |
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