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spacetelescope/pysynphot | pysynphot/locations.py | get_data_filename | def get_data_filename(filename):
"""Map filename to its actual path.
Parameters
----------
filename : str
Filename to search.
Returns
-------
path : str
Full path to the file in data directory.
"""
global _data_map
if _data_map is None:
_data_map = {}
... | python | def get_data_filename(filename):
"""Map filename to its actual path.
Parameters
----------
filename : str
Filename to search.
Returns
-------
path : str
Full path to the file in data directory.
"""
global _data_map
if _data_map is None:
_data_map = {}
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spacetelescope/pysynphot | pysynphot/renorm.py | StdRenorm | def StdRenorm(spectrum, band, RNval, RNunitstring, force=False):
"""This is used by `~pysynphot.spectrum.SourceSpectrum` for
renormalization.
Parameters
----------
spectrum : `~pysynphot.spectrum.SourceSpectrum`
Spectrum to renormalize.
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"""This is used by `~pysynphot.spectrum.SourceSpectrum` for
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Parameters
----------
spectrum : `~pysynphot.spectrum.SourceSpectrum`
Spectrum to renormalize.
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spacetelescope/pysynphot | commissioning/convert/convertcases.py | setdirs | def setdirs(outfiles):
"""Create the directories if need be"""
for k in outfiles:
fname=outfiles[k]
dname= os.path.dirname(fname)
if not os.path.isdir(dname):
os.mkdir(dname) | python | def setdirs(outfiles):
"""Create the directories if need be"""
for k in outfiles:
fname=outfiles[k]
dname= os.path.dirname(fname)
if not os.path.isdir(dname):
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spacetelescope/pysynphot | pysynphot/planck.py | bb_photlam_arcsec | def bb_photlam_arcsec(wave, temperature):
"""Evaluate Planck's law in ``photlam`` per square arcsec.
.. note::
Uses :func:`llam_SI` for calculation, and then converts
SI units back to CGS.
Parameters
----------
wave : array_like
Wavelength values in Angstrom.
temperat... | python | def bb_photlam_arcsec(wave, temperature):
"""Evaluate Planck's law in ``photlam`` per square arcsec.
.. note::
Uses :func:`llam_SI` for calculation, and then converts
SI units back to CGS.
Parameters
----------
wave : array_like
Wavelength values in Angstrom.
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spacetelescope/pysynphot | pysynphot/units.py | Units | def Units(uname):
"""Generate a unit object.
Parameters
----------
uname : str
Wavelength or flux unit name.
Returns
-------
unit : `BaseUnit` or `None`
Unit object. `None` means unitless.
Raises
------
ValueError
Unknown unit name.
"""
if isin... | python | def Units(uname):
"""Generate a unit object.
Parameters
----------
uname : str
Wavelength or flux unit name.
Returns
-------
unit : `BaseUnit` or `None`
Unit object. `None` means unitless.
Raises
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Unknown unit name.
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spacetelescope/pysynphot | pysynphot/units.py | ismatch | def ismatch(a,b):
"""Method to allow smart comparisons between classes, instances,
and string representations of units and give the right answer.
For internal use only."""
#Try the easy case
if a == b:
return True
else:
#Try isinstance in both orders
try:
if i... | python | def ismatch(a,b):
"""Method to allow smart comparisons between classes, instances,
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return True
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spacetelescope/pysynphot | pysynphot/units.py | Photlam.ToABMag | def ToABMag(self, wave, flux, **kwargs):
"""Convert to ``abmag``.
.. math::
\\textnormal{AB}_{\\nu} = -2.5 \\; \\log(h \\lambda \\; \\textnormal{photlam}) - 48.6
where :math:`h` is as defined in :ref:`pysynphot-constants`.
Parameters
----------
wave, flux ... | python | def ToABMag(self, wave, flux, **kwargs):
"""Convert to ``abmag``.
.. math::
\\textnormal{AB}_{\\nu} = -2.5 \\; \\log(h \\lambda \\; \\textnormal{photlam}) - 48.6
where :math:`h` is as defined in :ref:`pysynphot-constants`.
Parameters
----------
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spacetelescope/pysynphot | pysynphot/units.py | Photlam.ToSTMag | def ToSTMag(self, wave, flux, **kwargs):
"""Convert to ``stmag``.
.. math::
\\textnormal{ST}_{\\lambda} = -2.5 \\; \\log(\\frac{hc}{\\lambda} \\; \\textnormal{photlam}) - 21.1
where :math:`h` and :math:`c` are as defined in
:ref:`pysynphot-constants`.
Parameters
... | python | def ToSTMag(self, wave, flux, **kwargs):
"""Convert to ``stmag``.
.. math::
\\textnormal{ST}_{\\lambda} = -2.5 \\; \\log(\\frac{hc}{\\lambda} \\; \\textnormal{photlam}) - 21.1
where :math:`h` and :math:`c` are as defined in
:ref:`pysynphot-constants`.
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spacetelescope/pysynphot | pysynphot/units.py | Photlam.ToOBMag | def ToOBMag(self, wave, flux, area=None):
"""Convert to ``obmag``.
.. math::
\\textnormal{obmag} = -2.5 \\; \\log(\\delta \\lambda \\; \\times \\; \\textnormal{area} \\; \\times \\; \\textnormal{photlam})
where :math:`\\delta \\lambda` represent bin widths derived from
:f... | python | def ToOBMag(self, wave, flux, area=None):
"""Convert to ``obmag``.
.. math::
\\textnormal{obmag} = -2.5 \\; \\log(\\delta \\lambda \\; \\times \\; \\textnormal{area} \\; \\times \\; \\textnormal{photlam})
where :math:`\\delta \\lambda` represent bin widths derived from
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spacetelescope/pysynphot | pysynphot/units.py | Photlam.ToVegaMag | def ToVegaMag(self, wave, flux, **kwargs):
"""Convert to ``vegamag``.
.. math::
\\textnormal{vegamag} = -2.5 \\; \\log(\\frac{\\textnormal{photlam}}{f_{\\textnormal{Vega}}})
where :math:`f_{\\textnormal{Vega}}` is the flux of
:ref:`pysynphot-vega-spec` resampled at given w... | python | def ToVegaMag(self, wave, flux, **kwargs):
"""Convert to ``vegamag``.
.. math::
\\textnormal{vegamag} = -2.5 \\; \\log(\\frac{\\textnormal{photlam}}{f_{\\textnormal{Vega}}})
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geronimp/graftM | graftm/graftm_package.py | GraftMPackage.acquire | def acquire(graftm_package_path):
'''Acquire a new graftm Package
Parameters
----------
graftm_output_path: str
path to base directory of graftm
'''
contents_hash = json.load(
open(
... | python | def acquire(graftm_package_path):
'''Acquire a new graftm Package
Parameters
----------
graftm_output_path: str
path to base directory of graftm
'''
contents_hash = json.load(
open(
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geronimp/graftM | graftm/graftm_package.py | GraftMPackage.check_required_keys | def check_required_keys(self, required_keys):
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if key not in h:
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geronimp/graftM | graftm/graftm_package.py | GraftMPackageVersion2.compile | def compile(output_package_path, refpkg_path, hmm_path, diamond_database_file, max_range,
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geronimp/graftM | graftm/graftm_package.py | GraftMPackageVersion3.create_diamond_db | def create_diamond_db(self):
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Returns
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path to the created diamond db e.g. 'my_sequences.dmnd'
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cmd = "diamond makedb --in '%s' -d '... | python | def create_diamond_db(self):
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path to the created diamond db e.g. 'my_sequences.dmnd'
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geronimp/graftM | graftm/graftm_package.py | GraftMPackageVersion3.graftm_package_is_protein | def graftm_package_is_protein(graftm_package):
'''Return true if this package is an Amino Acid alignment package, otherwise
False i.e. it is a nucleotide package. In general it is best to use
'is_protein_package' instead.
'''
found = None
with open(graftm_package.alignme... | python | def graftm_package_is_protein(graftm_package):
'''Return true if this package is an Amino Acid alignment package, otherwise
False i.e. it is a nucleotide package. In general it is best to use
'is_protein_package' instead.
'''
found = None
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geronimp/graftM | graftm/graftm_package.py | GraftMPackageVersion3.is_protein_package | def is_protein_package(self):
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'''Return true if this package is an Amino Acid alignment package, otherwise
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geronimp/graftM | graftm/unpack_sequences.py | UnpackRawReads.basename | def basename(self):
'''Return the name of the file with the '.fasta' or 'fq.gz' etc
removed'''
return os.path.basename(self.read_file)[:-len(self._get_extension(self.read_file))] | python | def basename(self):
'''Return the name of the file with the '.fasta' or 'fq.gz' etc
removed'''
return os.path.basename(self.read_file)[:-len(self._get_extension(self.read_file))] | [
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geronimp/graftM | graftm/dendropy_tree_cleaner.py | DendropyTreeCleaner.match_alignment_and_tree_sequence_ids | def match_alignment_and_tree_sequence_ids(self, sequence_names, tree):
'''Check to make sure that the sequences specified in the alignment
and the tree are the same, otherwise raise an Exception detailing
the problem for the user to fix
Parameters
----------
sequence_nam... | python | def match_alignment_and_tree_sequence_ids(self, sequence_names, tree):
'''Check to make sure that the sequences specified in the alignment
and the tree are the same, otherwise raise an Exception detailing
the problem for the user to fix
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geronimp/graftM | graftm/dendropy_tree_cleaner.py | DendropyTreeCleaner.remove_sequences | def remove_sequences(self, tree, sequence_names):
'''Remove sequences with in the given sequence_names array from the tree in
place. Assumes the sequences are found in the tree, and that they are
all unique.
Parameters
----------
tree: dendropy.Tree
tree to r... | python | def remove_sequences(self, tree, sequence_names):
'''Remove sequences with in the given sequence_names array from the tree in
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geronimp/graftM | graftm/sequence_searcher.py | SequenceSearcher._hmmalign | def _hmmalign(self, input_path, directions, pipeline,
forward_reads_output_path, reverse_reads_output_path):
'''
Align reads to the aln_hmm. Receives unaligned sequences and
aligns them.
Parameters
----------
input_path : str
Filename of una... | python | def _hmmalign(self, input_path, directions, pipeline,
forward_reads_output_path, reverse_reads_output_path):
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Align reads to the aln_hmm. Receives unaligned sequences and
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Parameters
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input_path : str
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geronimp/graftM | graftm/sequence_searcher.py | SequenceSearcher.hmmalign_sequences | def hmmalign_sequences(self, hmm, sequences, output_file):
'''Run hmmalign and convert output to aligned fasta format
Parameters
----------
hmm: str
path to hmm file
sequences: str
path to file of sequences to be aligned
output_file: str
... | python | def hmmalign_sequences(self, hmm, sequences, output_file):
'''Run hmmalign and convert output to aligned fasta format
Parameters
----------
hmm: str
path to hmm file
sequences: str
path to file of sequences to be aligned
output_file: str
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geronimp/graftM | graftm/sequence_searcher.py | SequenceSearcher.hmmsearch | def hmmsearch(self, output_path, input_path, unpack, seq_type, threads, cutoff, orfm):
'''
hmmsearch - Search raw reads for hits using search_hmm list
Parameters
----------
output_path : str
path to output domtblout table
input_path : str
path to ... | python | def hmmsearch(self, output_path, input_path, unpack, seq_type, threads, cutoff, orfm):
'''
hmmsearch - Search raw reads for hits using search_hmm list
Parameters
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output_path : str
path to output domtblout table
input_path : str
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geronimp/graftM | graftm/sequence_searcher.py | SequenceSearcher.merge_forev_aln | def merge_forev_aln(self, forward_aln_list, reverse_aln_list, outputs):
'''
merge_forev_aln - Merges forward and reverse alignments for a given run
Parameters
----------
aln_list : array
List of the forward and reverse alignments for each of the runs
give... | python | def merge_forev_aln(self, forward_aln_list, reverse_aln_list, outputs):
'''
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aln_list : array
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geronimp/graftM | graftm/sequence_searcher.py | SequenceSearcher.nhmmer | def nhmmer(self, output_path, unpack, threads, evalue):
'''
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Parameters
----------
output_path : str
A string containing the path to the input sequences
unpack : obj
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A string containing the path to the input sequences
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geronimp/graftM | graftm/sequence_searcher.py | SequenceSearcher._check_euk_contamination | def _check_euk_contamination(self, hmm_hit_tables):
'''
check_euk_contamination - Check output HMM tables hits reads that hit
the 18S HMM with a higher bit score.
Parameters
----------
hmm_hit_tables : array
Array of paths to the out... | python | def _check_euk_contamination(self, hmm_hit_tables):
'''
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geronimp/graftM | graftm/sequence_searcher.py | SequenceSearcher._extract_multiple_hits | def _extract_multiple_hits(self, hits, reads_path, output_path):
'''
splits out regions of a read that hit the HMM. For example when two of
same gene are identified within the same contig, The regions mapping to
the HMM will be split out and written out to a new file as a new record.
... | python | def _extract_multiple_hits(self, hits, reads_path, output_path):
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geronimp/graftM | graftm/sequence_searcher.py | SequenceSearcher.alignment_correcter | def alignment_correcter(self, alignment_file_list, output_file_name,
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geronimp/graftM | graftm/sequence_searcher.py | SequenceSearcher._extract_orfs | def _extract_orfs(self, input_path, orfm, hit_readnames, output_path, search_method, sequence_frame_info_list=None):
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Call ORFs on a file with nucleotide sequences and extract the proteins
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input_path : str
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geronimp/graftM | graftm/sequence_searcher.py | SequenceSearcher.aa_db_search | def aa_db_search(self, files, base, unpack, search_method,
maximum_range, threads, evalue, min_orf_length,
restrict_read_length, diamond_database):
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geronimp/graftM | graftm/sequence_searcher.py | SequenceSearcher.nt_db_search | def nt_db_search(self, files, base, unpack, euk_check,
search_method, maximum_range, threads, evalue):
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Nucleotide database search pipeline - pipeline where reads are searched
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Nucleotide database search pipeline - pipeline where reads are searched
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geronimp/graftM | graftm/sequence_searcher.py | SequenceSearcher.align | def align(self, input_path, output_path, directions, pipeline,
filter_minimum):
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Parameters
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input_path : str
output_pa... | python | def align(self, input_path, output_path, directions, pipeline,
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geronimp/graftM | graftm/rerooter.py | Rerooter.reroot_by_tree | def reroot_by_tree(self, old_tree, new_tree):
'''reroot the new tree so that it matches the old tree's root, if
possible. If more than one rerooting is possible, root at the longest
internal branch that is consistent with the root of the old_tree.
Assumes that the tree is binary. Both ... | python | def reroot_by_tree(self, old_tree, new_tree):
'''reroot the new tree so that it matches the old tree's root, if
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geronimp/graftM | graftm/run.py | Run._assign_taxonomy_with_diamond | def _assign_taxonomy_with_diamond(self, base_list, db_search_results,
graftm_package, graftm_files):
'''Run diamond to assign taxonomy
Parameters
----------
base_list: list of str
list of sequence block names
db_search_results: l... | python | def _assign_taxonomy_with_diamond(self, base_list, db_search_results,
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base_list: list of str
list of sequence block names
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geronimp/graftM | graftm/update.py | Update._concatenate_file | def _concatenate_file(self, file_list, output):
'''
Call unix "cat" to concatenate a list of files
Parameters
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file_list: list
List of strings, each leading to a file. These files are the ones to
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["... | python | def _concatenate_file(self, file_list, output):
'''
Call unix "cat" to concatenate a list of files
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file_list: list
List of strings, each leading to a file. These files are the ones to
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geronimp/graftM | graftm/greengenes_taxonomy.py | GreenGenesTaxonomy.write | def write(self, output_io):
'''Write a taxonomy to an open stream out in GG format. Code calling this
function must open and close the io object.'''
for name, tax in self.taxonomy.items():
output_io.write("%s\t%s\n" % (name, '; '.join(tax))) | python | def write(self, output_io):
'''Write a taxonomy to an open stream out in GG format. Code calling this
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geronimp/graftM | graftm/decorator.py | Decorator._reroot | def _reroot(self):
'''Run the re-rooting algorithm in the Rerooter class.'''
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self.tree = rerooter.reroot_by_tree(self.reference_tree,
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geronimp/graftM | graftm/housekeeping.py | HouseKeeping.file_basename | def file_basename(self, file):
'''
Strips the path and last extension from the file variable. If the
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'''
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geronimp/graftM | graftm/housekeeping.py | HouseKeeping.set_euk_hmm | def set_euk_hmm(self, args):
'Set the hmm used by graftM to cross check for euks.'
if hasattr(args, 'euk_hmm_file'):
pass
elif not hasattr(args, 'euk_hmm_file'):
# set to path based on the location of bin/graftM, which has
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'Set the hmm used by graftM to cross check for euks.'
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geronimp/graftM | graftm/housekeeping.py | HouseKeeping.get_maximum_range | def get_maximum_range(self, hmm):
'''
If no maximum range has been specified, and if using a hmm search, a
maximum range can be determined by using the length of the HMM
Parameters
----------
hmm : str
path to hmm profile
Returns
-------
... | python | def get_maximum_range(self, hmm):
'''
If no maximum range has been specified, and if using a hmm search, a
maximum range can be determined by using the length of the HMM
Parameters
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hmm : str
path to hmm profile
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geronimp/graftM | graftm/pplacer.py | Pplacer.place | def place(self, reverse_pipe, seqs_list, resolve_placements, files, args,
slash_endings, tax_descr, clusterer):
'''
placement - This is the placement pipeline in GraftM, in aligned reads
are placed into phylogenetic trees, and the results interpreted.
... | python | def place(self, reverse_pipe, seqs_list, resolve_placements, files, args,
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geronimp/graftM | graftm/sequence_extractor.py | SequenceExtractor.extract | def extract(self, reads_to_extract, database_fasta_file, output_file):
'''Extract the reads_to_extract from the database_fasta_file and put them in
output_file.
Parameters
----------
reads_to_extract: Iterable of str
IDs of reads to be extracted
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reads_to_extract: Iterable of str
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geronimp/graftM | graftm/sequence_extractor.py | SequenceExtractor.extract_forward_and_reverse_complement | def extract_forward_and_reverse_complement(
self, forward_reads_to_extract, reverse_reads_to_extract, database_fasta_file,
output_file):
'''As per extract except also reverse complement the sequences.'''
self.extract(forward_reads_to_extract, database_fasta_file, output_file)
... | python | def extract_forward_and_reverse_complement(
self, forward_reads_to_extract, reverse_reads_to_extract, database_fasta_file,
output_file):
'''As per extract except also reverse complement the sequences.'''
self.extract(forward_reads_to_extract, database_fasta_file, output_file)
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geronimp/graftM | graftm/summarise.py | Stats_And_Summary.write_tabular_otu_table | def write_tabular_otu_table(self, sample_names, read_taxonomies, combined_output_otu_table_io):
'''A function that takes a hash of trusted placements, and compiles them
into an OTU-esque table.'''
delim = u'\t'
combined_output_otu_table_io.write(delim.join(['#ID',
... | python | def write_tabular_otu_table(self, sample_names, read_taxonomies, combined_output_otu_table_io):
'''A function that takes a hash of trusted placements, and compiles them
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geronimp/graftM | graftm/summarise.py | Stats_And_Summary.write_krona_plot | def write_krona_plot(self, sample_names, read_taxonomies, output_krona_filename):
'''Creates krona plot at the given location. Assumes the krona executable
ktImportText is available on the shell PATH'''
tempfiles = []
for n in sample_names:
tempfiles.append(tempfile.NamedTemp... | python | def write_krona_plot(self, sample_names, read_taxonomies, output_krona_filename):
'''Creates krona plot at the given location. Assumes the krona executable
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geronimp/graftM | graftm/clusterer.py | Clusterer.uncluster_annotations | def uncluster_annotations(self, input_annotations, reverse_pipe):
'''
Update the annotations hash provided by pplacer to include all
representatives within each cluster
Parameters
----------
input_annotations : hash
Classifications for each representative seq... | python | def uncluster_annotations(self, input_annotations, reverse_pipe):
'''
Update the annotations hash provided by pplacer to include all
representatives within each cluster
Parameters
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input_annotations : hash
Classifications for each representative seq... | [
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geronimp/graftM | graftm/clusterer.py | Clusterer.cluster | def cluster(self, input_fasta_list, reverse_pipe):
'''
cluster - Clusters reads at 100% identity level and writes them to
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Parameters
----------
input_fasta_list : list
l... | python | def cluster(self, input_fasta_list, reverse_pipe):
'''
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geronimp/graftM | graftm/archive.py | Archive.create | def create(self, input_package_path, output_package_path, **kwargs):
"""Create an archived GraftM package
Parameters
----------
input_package_path: str
path to gpkg to be archived
output_pacakge_path: str
output package path
kwargs:
fo... | python | def create(self, input_package_path, output_package_path, **kwargs):
"""Create an archived GraftM package
Parameters
----------
input_package_path: str
path to gpkg to be archived
output_pacakge_path: str
output package path
kwargs:
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geronimp/graftM | graftm/archive.py | Archive.extract | def extract(self, archive_path, output_package_path, **kwargs):
'''Extract an archived GraftM package.
Parameters
----------
archive_path: str
path to archive
output_package_path: str
path to where to put the extracted file
kwargs:
for... | python | def extract(self, archive_path, output_package_path, **kwargs):
'''Extract an archived GraftM package.
Parameters
----------
archive_path: str
path to archive
output_package_path: str
path to where to put the extracted file
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geronimp/graftM | graftm/archive.py | Archive._setup_output | def _setup_output(self, path, force):
'''Clear the way for an output to be placed at path'''
# Allow for special case of output being a pipe
if os.path.isdir(path) or os.path.isfile(path):
if force:
logging.warn("Deleting previous file/directory '%s'" % path)
... | python | def _setup_output(self, path, force):
'''Clear the way for an output to be placed at path'''
# Allow for special case of output being a pipe
if os.path.isdir(path) or os.path.isfile(path):
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geronimp/graftM | graftm/sequence_search_results.py | HMMSearchResult.import_from_nhmmer_table | def import_from_nhmmer_table(hmmout_path):
'''Generate new results object from the output of nhmmer search'''
# nhmmer format is
# qseqid queryname hmmfrom hmmto alifrom alito envfrom envto sqlen strand evalue bitscore bias description
# 0 2 4 5 6 7 8 ... | python | def import_from_nhmmer_table(hmmout_path):
'''Generate new results object from the output of nhmmer search'''
# nhmmer format is
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geronimp/graftM | graftm/hmmsearcher.py | HmmSearcher.hmmsearch | def hmmsearch(self, input_pipe, hmms, output_files):
r"""Run HMMsearch with all the HMMs, generating output files
Parameters
----------
input_pipe: String
A string which is a partial command line. When this command is run
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geronimp/graftM | graftm/hmmsearcher.py | HmmSearcher._munch_off_batch | def _munch_off_batch(self, queue):
r"""Take a batch of sequences off the queue, and return pairs_to_run.
The queue given as a parameter is affected
"""
# if the number of CPUs used == 1, just pop one off (which == below)
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r"""Take a batch of sequences off the queue, and return pairs_to_run.
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geronimp/graftM | graftm/hmmsearcher.py | HmmSearcher._hmm_command | def _hmm_command(self, input_pipe, pairs_to_run):
r"""INTERNAL method for getting cmdline for running a batch of HMMs.
Parameters
----------
input_pipe: as hmmsearch
pairs_to_run: list
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r"""INTERNAL method for getting cmdline for running a batch of HMMs.
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input_pipe: as hmmsearch
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geronimp/graftM | graftm/create.py | Create._parse_contents | def _parse_contents(self, contents_file_path):
'''
Parse the contents .json file and return the dictionary
Parameters
----------
contents_file_path: str
Path to file containing .json file to parse.
Returns
-------
contents_dict: dict
... | python | def _parse_contents(self, contents_file_path):
'''
Parse the contents .json file and return the dictionary
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contents_file_path: str
Path to file containing .json file to parse.
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geronimp/graftM | graftm/create.py | Create._check_reads_hit | def _check_reads_hit(self, alignment_io, min_aligned_fraction):
'''Given an alignment return a list of sequence names that are less
than the min_aligned_fraction'''
to_return = []
alignment_length = None
for s in SeqIO.parse(alignment_io, "fasta"):
if not alignment_le... | python | def _check_reads_hit(self, alignment_io, min_aligned_fraction):
'''Given an alignment return a list of sequence names that are less
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geronimp/graftM | graftm/create.py | Create._align_sequences | def _align_sequences(self, input_sequences_path, output_alignment_path,
threads):
'''Align sequences into alignment_file
Parameters
----------
input_sequences_path: str
path to input sequences in fasta format
output_alignment_path: str
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input_sequences_path: str
path to input sequences in fasta format
output_alignment_path: str
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geronimp/graftM | graftm/create.py | Create._get_hmm_from_alignment | def _get_hmm_from_alignment(self, alignment, hmm_filename, output_alignment_filename):
'''Return a HMM file and alignment of sequences to that HMM
Parameters
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alignment: str
path to aligned proteins
hmm_filename: str
write the hmm to this file p... | python | def _get_hmm_from_alignment(self, alignment, hmm_filename, output_alignment_filename):
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path to aligned proteins
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geronimp/graftM | graftm/create.py | Create._align_sequences_to_hmm | def _align_sequences_to_hmm(self, hmm_file, sequences_file, output_alignment_file):
'''Align sequences to an HMM, and write an alignment of
these proteins after cleanup so that they can be used for tree-making
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sequences_file: str
path to file of... | python | def _align_sequences_to_hmm(self, hmm_file, sequences_file, output_alignment_file):
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geronimp/graftM | graftm/create.py | Create._define_range | def _define_range(self, sequences):
'''
define_range - define the maximum range within which two hits in a db
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reads in the database.
Parameters
----------
sequences : str
A path t... | python | def _define_range(self, sequences):
'''
define_range - define the maximum range within which two hits in a db
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geronimp/graftM | graftm/create.py | Create._generate_tree_log_file | def _generate_tree_log_file(self, tree, alignment, output_tree_file_path,
output_log_file_path, residue_type, fasttree):
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made that tree
Returns
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geronimp/graftM | graftm/create.py | Create._remove_sequences_from_alignment | def _remove_sequences_from_alignment(self, sequence_names, input_alignment_file, output_alignment_file):
'''Remove sequences from the alignment file that have names in
sequence_names
Parameters
----------
sequence_names: list of str
names of sequences to remove
... | python | def _remove_sequences_from_alignment(self, sequence_names, input_alignment_file, output_alignment_file):
'''Remove sequences from the alignment file that have names in
sequence_names
Parameters
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sequence_names: list of str
names of sequences to remove
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geronimp/graftM | graftm/create.py | Create._create_dmnd_database | def _create_dmnd_database(self, unaligned_sequences_path, daa_output):
'''
Build a diamond database using diamond makedb
Parameters
----------
unaligned_sequences_path: str
path to a FASTA file containing unaligned sequences
daa_output: str
Name o... | python | def _create_dmnd_database(self, unaligned_sequences_path, daa_output):
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Build a diamond database using diamond makedb
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unaligned_sequences_path: str
path to a FASTA file containing unaligned sequences
daa_output: str
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geronimp/graftM | graftm/create.py | Create._check_for_duplicate_sequence_names | def _check_for_duplicate_sequence_names(self, fasta_file_path):
"""Test if the given fasta file contains sequences with duplicate
sequence names.
Parameters
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fasta_file_path: string
path to file that is to be checked
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fasta_file_path: string
path to file that is to be checked
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geronimp/graftM | graftm/getaxnseq.py | Getaxnseq.read_taxtastic_taxonomy_and_seqinfo | def read_taxtastic_taxonomy_and_seqinfo(self, taxonomy_io, seqinfo_io):
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geronimp/graftM | graftm/sequence_io.py | SequenceIO.each_sequence | def each_sequence(self, fp):
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for name, seq, _ in self.each(fp):
yield Sequence(name, seq) | python | def each_sequence(self, fp):
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bitly/asyncmongo | asyncmongo/pool.py | ConnectionPools.get_connection_pool | def get_connection_pool(self, pool_id, *args, **kwargs):
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:Parameters:
- `pool_id`: unique id for a connection pool
"""
assert isinstance(pool_id, (str, unicode))
if not hasattr(self, '_po... | python | def get_connection_pool(self, pool_id, *args, **kwargs):
"""get a connection pool, transparently creating it if it doesn't already exist
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bitly/asyncmongo | asyncmongo/pool.py | ConnectionPools.close_idle_connections | def close_idle_connections(self, pool_id=None):
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return
if pool_id:
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raise ProgrammingError("pool %r does not exist" % pool_id)
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bitly/asyncmongo | asyncmongo/cursor.py | Cursor.__query_options | def __query_options(self):
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djungelorm/sphinx-tabs | sphinx_tabs/tabs.py | update_context | def update_context(app, pagename, templatename, context, doctree):
""" Remove sphinx-tabs CSS and JS asset files if not used in a page """
if doctree is None:
return
visitor = _FindTabsDirectiveVisitor(doctree)
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""" Remove sphinx-tabs CSS and JS asset files if not used in a page """
if doctree is None:
return
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djungelorm/sphinx-tabs | sphinx_tabs/tabs.py | copy_assets | def copy_assets(app, exception):
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""" Copy asset files to the output """
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djungelorm/sphinx-tabs | sphinx_tabs/tabs.py | setup | def setup(app):
""" Set up the plugin """
app.add_config_value('sphinx_tabs_nowarn', False, '')
app.add_config_value('sphinx_tabs_valid_builders', [], '')
app.add_directive('tabs', TabsDirective)
app.add_directive('tab', TabDirective)
app.add_directive('group-tab', GroupTabDirective)
app.add... | python | def setup(app):
""" Set up the plugin """
app.add_config_value('sphinx_tabs_nowarn', False, '')
app.add_config_value('sphinx_tabs_valid_builders', [], '')
app.add_directive('tabs', TabsDirective)
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djungelorm/sphinx-tabs | sphinx_tabs/tabs.py | TabsDirective.run | def run(self):
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bitly/asyncmongo | asyncmongo/client.py | Client.connection | def connection(self, collectionname, dbname=None):
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raises `DataError` on names with unallowable characters.
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- `dbname`: (optional) overide the default db for a connection
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"""Get a cursor to a collection by name.
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bitly/asyncmongo | asyncmongo/client.py | Client.collection_names | def collection_names(self, callback):
"""Get a list of all the collection names in selected database"""
callback = partial(self._collection_names_result, callback)
self["system.namespaces"].find(_must_use_master=True, callback=callback) | python | def collection_names(self, callback):
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bitly/asyncmongo | asyncmongo/client.py | Client._collection_names_result | def _collection_names_result(self, callback, results, error=None):
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names = [r['name'] for r in results if r['name'].count('.') == 1]
assert error == None, repr(error)
strip = len(self._pool._dbname) + 1
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DBuildService/dockerfile-parse | dockerfile_parse/parser.py | DockerfileParser.parent_images | def parent_images(self, parents):
"""
setter for images in 'FROM' instructions.
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DBuildService/dockerfile-parse | dockerfile_parse/parser.py | DockerfileParser.baseimage | def baseimage(self, new_image):
"""
change image of final stage FROM instruction
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images[-1] = new_image
self.parent_images = images | python | def baseimage(self, new_image):
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change image of final stage FROM instruction
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DBuildService/dockerfile-parse | dockerfile_parse/parser.py | DockerfileParser.cmd | def cmd(self, value):
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cmd = None
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DBuildService/dockerfile-parse | dockerfile_parse/parser.py | DockerfileParser._instruction_getter | def _instruction_getter(self, name, env_replace):
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DBuildService/dockerfile-parse | dockerfile_parse/util.py | b2u | def b2u(string):
""" bytes to unicode """
if (isinstance(string, bytes) or
(PY2 and isinstance(string, str))):
return string.decode('utf-8')
return string | python | def b2u(string):
""" bytes to unicode """
if (isinstance(string, bytes) or
(PY2 and isinstance(string, str))):
return string.decode('utf-8')
return string | [
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DBuildService/dockerfile-parse | dockerfile_parse/util.py | u2b | def u2b(string):
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if ((PY2 and isinstance(string, unicode)) or
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DBuildService/dockerfile-parse | dockerfile_parse/util.py | WordSplitter._update_quoting_state | def _update_quoting_state(self, ch):
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Update self.quotes and self.escaped
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:return: ch if it was not used to update quoting state, else ''
"""
# Set whether the next character is escaped
# Unquoted:
# a backslash esc... | python | def _update_quoting_state(self, ch):
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Update self.quotes and self.escaped
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DBuildService/dockerfile-parse | dockerfile_parse/util.py | WordSplitter.split | def split(self, maxsplit=None, dequote=True):
"""
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"""
Generator for the words of the string
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DBuildService/dockerfile-parse | dockerfile_parse/util.py | Context.get_line_value | def get_line_value(self, context_type):
"""
Get the values defined on this line.
:param context_type: "ENV" or "LABEL"
:return: values of given type defined on this line
"""
if context_type.upper() == "ENV":
return self.line_envs
elif context_type.upp... | python | def get_line_value(self, context_type):
"""
Get the values defined on this line.
:param context_type: "ENV" or "LABEL"
:return: values of given type defined on this line
"""
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DBuildService/dockerfile-parse | dockerfile_parse/util.py | Context.get_values | def get_values(self, context_type):
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Get the values valid on this line.
:param context_type: "ENV" or "LABEL"
:return: values of given type valid on this line
"""
if context_type.upper() == "ENV":
return self.envs
elif context_type.upper() == "LABE... | python | def get_values(self, context_type):
"""
Get the values valid on this line.
:param context_type: "ENV" or "LABEL"
:return: values of given type valid on this line
"""
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gvanderheide/discreteMarkovChain | discreteMarkovChain/usefulFunctions.py | uniqueStates | def uniqueStates(states,rates):
"""
Returns unique states and sums up the corresponding rates.
States should be a 2d numpy array with on each row a state, and rates a 1d numpy array with length equal to the number of rows in states.
This may be helpful in the transition function for summing u... | python | def uniqueStates(states,rates):
"""
Returns unique states and sums up the corresponding rates.
States should be a 2d numpy array with on each row a state, and rates a 1d numpy array with length equal to the number of rows in states.
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gvanderheide/discreteMarkovChain | discreteMarkovChain/markovChain.py | markovChain.checkInitialState | def checkInitialState(self,initialState):
"""
Check whether the initial state is of the correct type.
The state should be either an int, list, tuple or np.array and all its elements must be integer.
Returns an int if the state is an integer, otherwise a tuple.
"""
assert ... | python | def checkInitialState(self,initialState):
"""
Check whether the initial state is of the correct type.
The state should be either an int, list, tuple or np.array and all its elements must be integer.
Returns an int if the state is an integer, otherwise a tuple.
"""
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gvanderheide/discreteMarkovChain | discreteMarkovChain/markovChain.py | markovChain.indirectInitialMatrix | def indirectInitialMatrix(self, initialState):
"""
Given some initial state, this iteratively determines new states.
We repeatedly call the transition function on unvisited states in the frontier set.
Each newly visited state is put in a dictionary called 'mapping' and the rates are stor... | python | def indirectInitialMatrix(self, initialState):
"""
Given some initial state, this iteratively determines new states.
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Each newly visited state is put in a dictionary called 'mapping' and the rates are stor... | [
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gvanderheide/discreteMarkovChain | discreteMarkovChain/markovChain.py | markovChain.getStateCode | def getStateCode(self,state):
"""
Calculates the state code for a specific state or set of states.
We transform the states so that they are nonnegative and take an inner product.
The resulting number is unique because we use numeral system with a large enough base.
... | python | def getStateCode(self,state):
"""
Calculates the state code for a specific state or set of states.
We transform the states so that they are nonnegative and take an inner product.
The resulting number is unique because we use numeral system with a large enough base.
... | [
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gvanderheide/discreteMarkovChain | discreteMarkovChain/markovChain.py | markovChain.getStateIndex | def getStateIndex(self,state):
"""
Returns the index of a state by calculating the state code and searching for this code a sorted list.
Can be called on multiple states at once.
"""
statecodes = self.getStateCode(state)
return np.searchsorted(self.codes,statecodes).astyp... | python | def getStateIndex(self,state):
"""
Returns the index of a state by calculating the state code and searching for this code a sorted list.
Can be called on multiple states at once.
"""
statecodes = self.getStateCode(state)
return np.searchsorted(self.codes,statecodes).astyp... | [
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gvanderheide/discreteMarkovChain | discreteMarkovChain/markovChain.py | markovChain.transitionStates | def transitionStates(self,state):
"""
Return the indices of new states and their rates.
"""
newstates,rates = self.transition(state)
newindices = self.getStateIndex(newstates)
return newindices,rates | python | def transitionStates(self,state):
"""
Return the indices of new states and their rates.
"""
newstates,rates = self.transition(state)
newindices = self.getStateIndex(newstates)
return newindices,rates | [
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gvanderheide/discreteMarkovChain | discreteMarkovChain/markovChain.py | markovChain.convertToRateMatrix | def convertToRateMatrix(self, Q):
"""
Converts the initial matrix to a rate matrix.
We make all rows in Q sum to zero by subtracting the row sums from the diagonal.
"""
rowSums = Q.sum(axis=1).getA1()
idxRange = np.arange(Q.shape[0])
Qdiag ... | python | def convertToRateMatrix(self, Q):
"""
Converts the initial matrix to a rate matrix.
We make all rows in Q sum to zero by subtracting the row sums from the diagonal.
"""
rowSums = Q.sum(axis=1).getA1()
idxRange = np.arange(Q.shape[0])
Qdiag ... | [
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gvanderheide/discreteMarkovChain | discreteMarkovChain/markovChain.py | markovChain.getTransitionMatrix | def getTransitionMatrix(self,probabilities=True):
"""
If self.P has been given already, we will reuse it and convert it to a sparse csr matrix if needed.
Otherwise, we will generate it using the direct or indirect method.
Since most solution methods use a probability matrix, thi... | python | def getTransitionMatrix(self,probabilities=True):
"""
If self.P has been given already, we will reuse it and convert it to a sparse csr matrix if needed.
Otherwise, we will generate it using the direct or indirect method.
Since most solution methods use a probability matrix, thi... | [
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