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SBRG/ssbio | ssbio/protein/structure/structprop.py | StructProp.find_disulfide_bridges | def find_disulfide_bridges(self, threshold=3.0):
"""Run Biopython's search_ss_bonds to find potential disulfide bridges for each chain and store in ChainProp.
Will add a list of tuple pairs into the annotations field, looks like this::
[ ((' ', 79, ' '), (' ', 110, ' ')),
(('... | python | def find_disulfide_bridges(self, threshold=3.0):
"""Run Biopython's search_ss_bonds to find potential disulfide bridges for each chain and store in ChainProp.
Will add a list of tuple pairs into the annotations field, looks like this::
[ ((' ', 79, ' '), (' ', 110, ' ')),
(('... | [
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SBRG/ssbio | ssbio/protein/structure/structprop.py | StructProp.get_polypeptide_within | def get_polypeptide_within(self, chain_id, resnum, angstroms, only_protein=True,
use_ca=False, custom_coord=None, return_resnums=False):
"""Get a Polypeptide object of the amino acids within X angstroms of the specified chain + residue number.
Args:
resnum (in... | python | def get_polypeptide_within(self, chain_id, resnum, angstroms, only_protein=True,
use_ca=False, custom_coord=None, return_resnums=False):
"""Get a Polypeptide object of the amino acids within X angstroms of the specified chain + residue number.
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resnum (in... | [
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SBRG/ssbio | ssbio/protein/structure/structprop.py | StructProp.get_seqprop_within | def get_seqprop_within(self, chain_id, resnum, angstroms, only_protein=True,
use_ca=False, custom_coord=None, return_resnums=False):
"""Get a SeqProp object of the amino acids within X angstroms of the specified chain + residue number.
Args:
resnum (int): Residue ... | python | def get_seqprop_within(self, chain_id, resnum, angstroms, only_protein=True,
use_ca=False, custom_coord=None, return_resnums=False):
"""Get a SeqProp object of the amino acids within X angstroms of the specified chain + residue number.
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SBRG/ssbio | ssbio/protein/structure/structprop.py | StructProp.get_dssp_annotations | def get_dssp_annotations(self, outdir, force_rerun=False):
"""Run DSSP on this structure and store the DSSP annotations in the corresponding ChainProp SeqRecords
Calculations are stored in the ChainProp's ``letter_annotations`` at the following keys:
* ``SS-dssp``
* ``RSA-dssp`... | python | def get_dssp_annotations(self, outdir, force_rerun=False):
"""Run DSSP on this structure and store the DSSP annotations in the corresponding ChainProp SeqRecords
Calculations are stored in the ChainProp's ``letter_annotations`` at the following keys:
* ``SS-dssp``
* ``RSA-dssp`... | [
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SBRG/ssbio | ssbio/protein/structure/structprop.py | StructProp.get_freesasa_annotations | def get_freesasa_annotations(self, outdir, include_hetatms=False, force_rerun=False):
"""Run ``freesasa`` on this structure and store the calculated properties in the corresponding ChainProps
"""
if self.file_type != 'pdb':
log.error('{}: unable to run freesasa with "{}" file type. P... | python | def get_freesasa_annotations(self, outdir, include_hetatms=False, force_rerun=False):
"""Run ``freesasa`` on this structure and store the calculated properties in the corresponding ChainProps
"""
if self.file_type != 'pdb':
log.error('{}: unable to run freesasa with "{}" file type. P... | [
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SBRG/ssbio | ssbio/protein/structure/structprop.py | StructProp.view_structure | def view_structure(self, only_chains=None, opacity=1.0, recolor=False, gui=False):
"""Use NGLviewer to display a structure in a Jupyter notebook
Args:
only_chains (str, list): Chain ID or IDs to display
opacity (float): Opacity of the structure
recolor (bool): If str... | python | def view_structure(self, only_chains=None, opacity=1.0, recolor=False, gui=False):
"""Use NGLviewer to display a structure in a Jupyter notebook
Args:
only_chains (str, list): Chain ID or IDs to display
opacity (float): Opacity of the structure
recolor (bool): If str... | [
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SBRG/ssbio | ssbio/protein/sequence/properties/tmhmm.py | label_TM_tmhmm_residue_numbers_and_leaflets | def label_TM_tmhmm_residue_numbers_and_leaflets(tmhmm_seq):
"""Determine the residue numbers of the TM-helix residues that cross the membrane and label them by leaflet.
Args:
tmhmm_seq: g.protein.representative_sequence.seq_record.letter_annotations['TM-tmhmm']
Returns:
leaflet_dict: a dic... | python | def label_TM_tmhmm_residue_numbers_and_leaflets(tmhmm_seq):
"""Determine the residue numbers of the TM-helix residues that cross the membrane and label them by leaflet.
Args:
tmhmm_seq: g.protein.representative_sequence.seq_record.letter_annotations['TM-tmhmm']
Returns:
leaflet_dict: a dic... | [
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SBRG/ssbio | ssbio/protein/sequence/properties/residues.py | biopython_protein_scale | def biopython_protein_scale(inseq, scale, custom_scale_dict=None, window=7):
"""Use Biopython to calculate properties using a sliding window over a sequence given a specific scale to use."""
if scale == 'kd_hydrophobicity':
scale_dict = kd_hydrophobicity_one
elif scale == 'bulkiness':
scale... | python | def biopython_protein_scale(inseq, scale, custom_scale_dict=None, window=7):
"""Use Biopython to calculate properties using a sliding window over a sequence given a specific scale to use."""
if scale == 'kd_hydrophobicity':
scale_dict = kd_hydrophobicity_one
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SBRG/ssbio | ssbio/protein/sequence/properties/residues.py | biopython_protein_analysis | def biopython_protein_analysis(inseq):
"""Utiize Biopython's ProteinAnalysis module to return general sequence properties of an amino acid string.
For full definitions see: http://biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html
Args:
inseq: Amino acid sequence
Re... | python | def biopython_protein_analysis(inseq):
"""Utiize Biopython's ProteinAnalysis module to return general sequence properties of an amino acid string.
For full definitions see: http://biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html
Args:
inseq: Amino acid sequence
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SBRG/ssbio | ssbio/protein/sequence/properties/residues.py | emboss_pepstats_on_fasta | def emboss_pepstats_on_fasta(infile, outfile='', outdir='', outext='.pepstats', force_rerun=False):
"""Run EMBOSS pepstats on a FASTA file.
Args:
infile: Path to FASTA file
outfile: Name of output file without extension
outdir: Path to output directory
outext: Extension of resul... | python | def emboss_pepstats_on_fasta(infile, outfile='', outdir='', outext='.pepstats', force_rerun=False):
"""Run EMBOSS pepstats on a FASTA file.
Args:
infile: Path to FASTA file
outfile: Name of output file without extension
outdir: Path to output directory
outext: Extension of resul... | [
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SBRG/ssbio | ssbio/protein/sequence/properties/residues.py | emboss_pepstats_parser | def emboss_pepstats_parser(infile):
"""Get dictionary of pepstats results.
Args:
infile: Path to pepstats outfile
Returns:
dict: Parsed information from pepstats
TODO:
Only currently parsing the bottom of the file for percentages of properties.
"""
with open(infile) a... | python | def emboss_pepstats_parser(infile):
"""Get dictionary of pepstats results.
Args:
infile: Path to pepstats outfile
Returns:
dict: Parsed information from pepstats
TODO:
Only currently parsing the bottom of the file for percentages of properties.
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SBRG/ssbio | ssbio/pipeline/atlas.py | ATLAS.load_strain | def load_strain(self, strain_id, strain_genome_file):
"""Load a strain as a new GEM-PRO by its ID and associated genome file. Stored in the ``strains`` attribute.
Args:
strain_id (str): Strain ID
strain_genome_file (str): Path to strain genome file
"""
# logging... | python | def load_strain(self, strain_id, strain_genome_file):
"""Load a strain as a new GEM-PRO by its ID and associated genome file. Stored in the ``strains`` attribute.
Args:
strain_id (str): Strain ID
strain_genome_file (str): Path to strain genome file
"""
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SBRG/ssbio | ssbio/pipeline/atlas.py | ATLAS.download_patric_genomes | def download_patric_genomes(self, ids, force_rerun=False):
"""Download genome files from PATRIC given a list of PATRIC genome IDs and load them as strains.
Args:
ids (str, list): PATRIC ID or list of PATRIC IDs
force_rerun (bool): If genome files should be downloaded again even ... | python | def download_patric_genomes(self, ids, force_rerun=False):
"""Download genome files from PATRIC given a list of PATRIC genome IDs and load them as strains.
Args:
ids (str, list): PATRIC ID or list of PATRIC IDs
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SBRG/ssbio | ssbio/pipeline/atlas.py | ATLAS._pare_down_model | def _pare_down_model(self, strain_gempro, genes_to_remove):
"""Mark genes as non-functional in a GEM-PRO. If there is a COBRApy model associated with it, the
COBRApy method delete_model_genes is utilized to delete genes.
Args:
strain_gempro (GEMPRO): GEMPRO object
ge... | python | def _pare_down_model(self, strain_gempro, genes_to_remove):
"""Mark genes as non-functional in a GEM-PRO. If there is a COBRApy model associated with it, the
COBRApy method delete_model_genes is utilized to delete genes.
Args:
strain_gempro (GEMPRO): GEMPRO object
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SBRG/ssbio | ssbio/pipeline/atlas.py | ATLAS._load_strain_sequences | def _load_strain_sequences(self, strain_gempro):
"""Load strain sequences from the orthology matrix into the base model for comparisons, and into the
strain-specific model itself.
"""
if self._orthology_matrix_has_sequences: # Load directly from the orthology matrix if it contains sequ... | python | def _load_strain_sequences(self, strain_gempro):
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SBRG/ssbio | ssbio/pipeline/atlas.py | ATLAS.build_strain_specific_models | def build_strain_specific_models(self, save_models=False):
"""Using the orthologous genes matrix, create and modify the strain specific models based on if orthologous
genes exist.
Also store the sequences directly in the reference GEM-PRO protein sequence attribute for the strains.
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"""Using the orthologous genes matrix, create and modify the strain specific models based on if orthologous
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Also store the sequences directly in the reference GEM-PRO protein sequence attribute for the strains.
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SBRG/ssbio | ssbio/pipeline/atlas.py | ATLAS.align_orthologous_genes_pairwise | def align_orthologous_genes_pairwise(self, gapopen=10, gapextend=0.5):
"""For each gene in the base strain, run a pairwise alignment for all orthologous gene sequences to it."""
for ref_gene in tqdm(self.reference_gempro.genes):
if len(ref_gene.protein.sequences) > 1:
alignme... | python | def align_orthologous_genes_pairwise(self, gapopen=10, gapextend=0.5):
"""For each gene in the base strain, run a pairwise alignment for all orthologous gene sequences to it."""
for ref_gene in tqdm(self.reference_gempro.genes):
if len(ref_gene.protein.sequences) > 1:
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SBRG/ssbio | ssbio/pipeline/atlas.py | ATLAS.get_atlas_per_gene_mutation_df | def get_atlas_per_gene_mutation_df(self, gene_id):
"""Create a single data frame which summarizes a gene and its mutations.
Args:
gene_id (str): Gene ID in the base model
Returns:
DataFrame: Pandas DataFrame of the results
"""
# TODO: also count: number... | python | def get_atlas_per_gene_mutation_df(self, gene_id):
"""Create a single data frame which summarizes a gene and its mutations.
Args:
gene_id (str): Gene ID in the base model
Returns:
DataFrame: Pandas DataFrame of the results
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SBRG/ssbio | ssbio/viz/nglview.py | add_residues_highlight_to_nglview | def add_residues_highlight_to_nglview(view, structure_resnums, chain, res_color='red'):
"""Add a residue number or numbers to an NGLWidget view object.
Args:
view (NGLWidget): NGLWidget view object
structure_resnums (int, list): Residue number(s) to highlight, structure numbering
chain ... | python | def add_residues_highlight_to_nglview(view, structure_resnums, chain, res_color='red'):
"""Add a residue number or numbers to an NGLWidget view object.
Args:
view (NGLWidget): NGLWidget view object
structure_resnums (int, list): Residue number(s) to highlight, structure numbering
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SBRG/ssbio | ssbio/databases/kegg.py | download_kegg_gene_metadata | def download_kegg_gene_metadata(gene_id, outdir=None, force_rerun=False):
"""Download the KEGG flatfile for a KEGG ID and return the path.
Args:
gene_id: KEGG gene ID (with organism code), i.e. "eco:1244"
outdir: optional output directory of metadata
Returns:
Path to metadata file
... | python | def download_kegg_gene_metadata(gene_id, outdir=None, force_rerun=False):
"""Download the KEGG flatfile for a KEGG ID and return the path.
Args:
gene_id: KEGG gene ID (with organism code), i.e. "eco:1244"
outdir: optional output directory of metadata
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Path to metadata file
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SBRG/ssbio | ssbio/databases/kegg.py | parse_kegg_gene_metadata | def parse_kegg_gene_metadata(infile):
"""Parse the KEGG flatfile and return a dictionary of metadata.
Dictionary keys are:
refseq
uniprot
pdbs
taxonomy
Args:
infile: Path to KEGG flatfile
Returns:
dict: Dictionary of metadata
"""
metadata = def... | python | def parse_kegg_gene_metadata(infile):
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infile: Path to KEGG flatfile
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SBRG/ssbio | ssbio/databases/kegg.py | map_kegg_all_genes | def map_kegg_all_genes(organism_code, target_db):
"""Map all of an organism's gene IDs to the target database.
This is faster than supplying a specific list of genes to map,
plus there seems to be a limit on the number you can map with a manual REST query anyway.
Args:
organism_code: the three... | python | def map_kegg_all_genes(organism_code, target_db):
"""Map all of an organism's gene IDs to the target database.
This is faster than supplying a specific list of genes to map,
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SBRG/ssbio | ssbio/protein/structure/homology/itasser/itasserprep.py | ITASSERPrep.prep_folder | def prep_folder(self, seq):
"""Take in a sequence string and prepares the folder for the I-TASSER run."""
itasser_dir = op.join(self.root_dir, self.id)
if not op.exists(itasser_dir):
os.makedirs(itasser_dir)
tmp = {self.id: seq}
fasta.write_fasta_file_from_dict(ind... | python | def prep_folder(self, seq):
"""Take in a sequence string and prepares the folder for the I-TASSER run."""
itasser_dir = op.join(self.root_dir, self.id)
if not op.exists(itasser_dir):
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SBRG/ssbio | ssbio/protein/sequence/utils/blast.py | run_makeblastdb | def run_makeblastdb(infile, dbtype, outdir=''):
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Args:
infile (str): path to genome FASTA file
dbtype (str): "nucl" or "prot" - what format your genome files are in
outdir (str): path to directory to output database files (default is original... | python | def run_makeblastdb(infile, dbtype, outdir=''):
"""Make the BLAST database for a genome file.
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SBRG/ssbio | ssbio/protein/sequence/utils/blast.py | run_bidirectional_blast | def run_bidirectional_blast(reference, other_genome, dbtype, outdir=''):
"""BLAST a genome against another, and vice versa.
This function requires BLAST to be installed, do so by running:
sudo apt install ncbi-blast+
Args:
reference (str): path to "reference" genome, aka your "base strain"
... | python | def run_bidirectional_blast(reference, other_genome, dbtype, outdir=''):
"""BLAST a genome against another, and vice versa.
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sudo apt install ncbi-blast+
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reference (str): path to "reference" genome, aka your "base strain"
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SBRG/ssbio | ssbio/protein/sequence/utils/blast.py | print_run_bidirectional_blast | def print_run_bidirectional_blast(reference, other_genome, dbtype, outdir):
"""Write torque submission files for running bidirectional blast on a server and print execution command.
Args:
reference (str): Path to "reference" genome, aka your "base strain"
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SBRG/ssbio | ssbio/protein/structure/utils/structureio.py | StructureIO.write_pdb | def write_pdb(self, custom_name='', out_suffix='', out_dir=None, custom_selection=None, force_rerun=False):
"""Write a new PDB file for the Structure's FIRST MODEL.
Set custom_selection to a PDB.Select class for custom SMCRA selections.
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SBRG/ssbio | ssbio/biopython/Bio/Struct/WWW/WHATIFXML.py | XMLParser._handle_builder_exception | def _handle_builder_exception(self, message, residue):
"""
Makes a PDB Construction Error a bit more verbose and informative
"""
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SBRG/ssbio | ssbio/biopython/Bio/Struct/WWW/WHATIFXML.py | XMLParser._parse | def _parse(self):
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SBRG/ssbio | ssbio/pipeline/atlas2.py | calculate_residue_counts_perstrain | def calculate_residue_counts_perstrain(protein_pickle_path, outdir, pdbflex_keys_file, wt_pid_cutoff=None, force_rerun=False):
"""Writes out a feather file for a PROTEIN counting amino acid occurences for ALL STRAINS along with SUBSEQUENCES"""
from collections import defaultdict
from ssbio.protein.sequence.... | python | def calculate_residue_counts_perstrain(protein_pickle_path, outdir, pdbflex_keys_file, wt_pid_cutoff=None, force_rerun=False):
"""Writes out a feather file for a PROTEIN counting amino acid occurences for ALL STRAINS along with SUBSEQUENCES"""
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SBRG/ssbio | ssbio/pipeline/atlas2.py | ATLAS2.filter_genes_and_strains | def filter_genes_and_strains(self, remove_genes_not_in_reference_model=True,
remove_strains_with_no_orthology=True, remove_strains_with_no_differences=False,
custom_keep_strains=None, custom_keep_genes=None):
"""Filters the analysis by keeping a ... | python | def filter_genes_and_strains(self, remove_genes_not_in_reference_model=True,
remove_strains_with_no_orthology=True, remove_strains_with_no_differences=False,
custom_keep_strains=None, custom_keep_genes=None):
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SBRG/ssbio | ssbio/pipeline/atlas2.py | ATLAS2._write_strain_functional_genes | def _write_strain_functional_genes(self, strain_id, ref_functional_genes, orth_matrix, force_rerun=False):
"""Create strain functional genes json file"""
func_genes_path = op.join(self.model_dir, '{}_funcgenes.json'.format(strain_id))
if ssbio.utils.force_rerun(flag=force_rerun, outfile=func_ge... | python | def _write_strain_functional_genes(self, strain_id, ref_functional_genes, orth_matrix, force_rerun=False):
"""Create strain functional genes json file"""
func_genes_path = op.join(self.model_dir, '{}_funcgenes.json'.format(strain_id))
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SBRG/ssbio | ssbio/pipeline/atlas2.py | ATLAS2.write_strain_functional_genes | def write_strain_functional_genes(self, force_rerun=False):
"""Wrapper function for _write_strain_functional_genes"""
if len(self.df_orthology_matrix) == 0:
raise RuntimeError('Empty orthology matrix, please calculate first!')
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raise RuntimeError('Empty orthology matrix, please calculate first!')
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SBRG/ssbio | ssbio/pipeline/atlas2.py | ATLAS2._build_strain_specific_model | def _build_strain_specific_model(self, strain_id, ref_functional_genes, orth_matrix, force_rerun=False):
"""Create strain GEMPRO, set functional genes"""
gp_noseqs_path = op.join(self.model_dir, '{}_gp.pckl'.format(strain_id))
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"""Create strain GEMPRO, set functional genes"""
gp_noseqs_path = op.join(self.model_dir, '{}_gp.pckl'.format(strain_id))
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SBRG/ssbio | ssbio/pipeline/atlas2.py | ATLAS2.build_strain_specific_models | def build_strain_specific_models(self, joblib=False, cores=1, force_rerun=False):
"""Wrapper function for _build_strain_specific_model"""
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"""Wrapper function for _build_strain_specific_model"""
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SBRG/ssbio | ssbio/pipeline/atlas2.py | ATLAS2._load_sequences_to_strain | def _load_sequences_to_strain(self, strain_id, force_rerun=False):
"""Load strain GEMPRO with functional genes defined, load sequences to it, save as new GEMPRO"""
gp_seqs_path = op.join(self.model_dir, '{}_gp_withseqs.pckl'.format(strain_id))
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"""Load strain GEMPRO with functional genes defined, load sequences to it, save as new GEMPRO"""
gp_seqs_path = op.join(self.model_dir, '{}_gp_withseqs.pckl'.format(strain_id))
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SBRG/ssbio | ssbio/pipeline/atlas2.py | ATLAS2.load_sequences_to_strains | def load_sequences_to_strains(self, joblib=False, cores=1, force_rerun=False):
"""Wrapper function for _load_sequences_to_strain"""
log.info('Loading sequences to strain GEM-PROs...')
if joblib:
result = DictList(Parallel(n_jobs=cores)(delayed(self._load_sequences_to_strain)(s, force... | python | def load_sequences_to_strains(self, joblib=False, cores=1, force_rerun=False):
"""Wrapper function for _load_sequences_to_strain"""
log.info('Loading sequences to strain GEM-PROs...')
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SBRG/ssbio | ssbio/pipeline/atlas2.py | ATLAS2._load_sequences_to_reference_gene | def _load_sequences_to_reference_gene(self, g_id, force_rerun=False):
"""Load orthologous strain sequences to reference Protein object, save as new pickle"""
protein_seqs_pickle_path = op.join(self.sequences_by_gene_dir, '{}_protein_withseqs.pckl'.format(g_id))
if ssbio.utils.force_rerun(flag=f... | python | def _load_sequences_to_reference_gene(self, g_id, force_rerun=False):
"""Load orthologous strain sequences to reference Protein object, save as new pickle"""
protein_seqs_pickle_path = op.join(self.sequences_by_gene_dir, '{}_protein_withseqs.pckl'.format(g_id))
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SBRG/ssbio | ssbio/pipeline/atlas2.py | ATLAS2.load_sequences_to_reference | def load_sequences_to_reference(self, sc=None, force_rerun=False):
"""Wrapper for _load_sequences_to_reference_gene"""
log.info('Loading sequences to reference GEM-PRO...')
from random import shuffle
g_ids = [g.id for g in self.reference_gempro.functional_genes]
shuffle(g_ids)
... | python | def load_sequences_to_reference(self, sc=None, force_rerun=False):
"""Wrapper for _load_sequences_to_reference_gene"""
log.info('Loading sequences to reference GEM-PRO...')
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g_ids = [g.id for g in self.reference_gempro.functional_genes]
shuffle(g_ids)
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SBRG/ssbio | ssbio/pipeline/atlas2.py | ATLAS2.store_disorder | def store_disorder(self, sc=None, force_rerun=False):
"""Wrapper for _store_disorder"""
log.info('Loading sequences to reference GEM-PRO...')
from random import shuffle
g_ids = [g.id for g in self.reference_gempro.functional_genes]
shuffle(g_ids)
def _store_disorder_sc(g... | python | def store_disorder(self, sc=None, force_rerun=False):
"""Wrapper for _store_disorder"""
log.info('Loading sequences to reference GEM-PRO...')
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g_ids = [g.id for g in self.reference_gempro.functional_genes]
shuffle(g_ids)
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SBRG/ssbio | ssbio/pipeline/atlas2.py | ATLAS2._align_orthologous_gene_pairwise | def _align_orthologous_gene_pairwise(self, g_id, gapopen=10, gapextend=0.5, engine='needle', parse=True, force_rerun=False):
"""Align orthologous strain sequences to representative Protein sequence, save as new pickle"""
protein_seqs_aln_pickle_path = op.join(self.sequences_by_gene_dir, '{}_protein_with... | python | def _align_orthologous_gene_pairwise(self, g_id, gapopen=10, gapextend=0.5, engine='needle', parse=True, force_rerun=False):
"""Align orthologous strain sequences to representative Protein sequence, save as new pickle"""
protein_seqs_aln_pickle_path = op.join(self.sequences_by_gene_dir, '{}_protein_with... | [
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SBRG/ssbio | ssbio/pipeline/atlas2.py | ATLAS2.align_orthologous_genes_pairwise | def align_orthologous_genes_pairwise(self, sc=None, joblib=False, cores=1, gapopen=10, gapextend=0.5,
engine='needle', parse=True, force_rerun=False):
"""Wrapper for _align_orthologous_gene_pairwise"""
log.info('Aligning sequences to reference GEM-PRO...')
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"""Wrapper for _align_orthologous_gene_pairwise"""
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SBRG/ssbio | ssbio/protein/sequence/utils/utils.py | cast_to_str | def cast_to_str(obj):
"""Return a string representation of a Seq or SeqRecord.
Args:
obj (str, Seq, SeqRecord): Biopython Seq or SeqRecord
Returns:
str: String representation of the sequence
"""
if isinstance(obj, str):
return obj
if isinstance(obj, Seq):
retu... | python | def cast_to_str(obj):
"""Return a string representation of a Seq or SeqRecord.
Args:
obj (str, Seq, SeqRecord): Biopython Seq or SeqRecord
Returns:
str: String representation of the sequence
"""
if isinstance(obj, str):
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SBRG/ssbio | ssbio/protein/sequence/utils/utils.py | cast_to_seq | def cast_to_seq(obj, alphabet=IUPAC.extended_protein):
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Args:
obj (str, Seq, SeqRecord): Sequence string or Biopython SeqRecord object
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"""Return a Seq representation of a string or SeqRecord object.
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SBRG/ssbio | ssbio/protein/sequence/utils/utils.py | cast_to_seq_record | def cast_to_seq_record(obj, alphabet=IUPAC.extended_protein, id="<unknown id>", name="<unknown name>",
description="<unknown description>", dbxrefs=None,
features=None, annotations=None,
letter_annotations=None):
"""Return a SeqRecord representati... | python | def cast_to_seq_record(obj, alphabet=IUPAC.extended_protein, id="<unknown id>", name="<unknown name>",
description="<unknown description>", dbxrefs=None,
features=None, annotations=None,
letter_annotations=None):
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SBRG/ssbio | ssbio/protein/sequence/utils/fasta.py | write_fasta_file | def write_fasta_file(seq_records, outname, outdir=None, outext='.faa', force_rerun=False):
"""Write a FASTA file for a SeqRecord or a list of SeqRecord objects.
Args:
seq_records (SeqRecord, list): SeqRecord or a list of SeqRecord objects
outname: Name of the output file which will have outext ... | python | def write_fasta_file(seq_records, outname, outdir=None, outext='.faa', force_rerun=False):
"""Write a FASTA file for a SeqRecord or a list of SeqRecord objects.
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SBRG/ssbio | ssbio/protein/sequence/utils/fasta.py | write_fasta_file_from_dict | def write_fasta_file_from_dict(indict, outname, outdir=None, outext='.faa', force_rerun=False):
"""Write a FASTA file for a dictionary of IDs and their sequence strings.
Args:
indict: Input dictionary with keys as IDs and values as sequence strings
outname: Name of the output file which will ha... | python | def write_fasta_file_from_dict(indict, outname, outdir=None, outext='.faa', force_rerun=False):
"""Write a FASTA file for a dictionary of IDs and their sequence strings.
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indict: Input dictionary with keys as IDs and values as sequence strings
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SBRG/ssbio | ssbio/protein/sequence/utils/fasta.py | write_seq_as_temp_fasta | def write_seq_as_temp_fasta(seq):
"""Write a sequence as a temporary FASTA file
Args:
seq (str, Seq, SeqRecord): Sequence string, Biopython Seq or SeqRecord object
Returns:
str: Path to temporary FASTA file (located in system temporary files directory)
"""
sr = ssbio.protein.seque... | python | def write_seq_as_temp_fasta(seq):
"""Write a sequence as a temporary FASTA file
Args:
seq (str, Seq, SeqRecord): Sequence string, Biopython Seq or SeqRecord object
Returns:
str: Path to temporary FASTA file (located in system temporary files directory)
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SBRG/ssbio | ssbio/protein/sequence/utils/fasta.py | load_fasta_file | def load_fasta_file(filename):
"""Load a FASTA file and return the sequences as a list of SeqRecords
Args:
filename (str): Path to the FASTA file to load
Returns:
list: list of all sequences in the FASTA file as Biopython SeqRecord objects
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... | python | def load_fasta_file(filename):
"""Load a FASTA file and return the sequences as a list of SeqRecords
Args:
filename (str): Path to the FASTA file to load
Returns:
list: list of all sequences in the FASTA file as Biopython SeqRecord objects
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SBRG/ssbio | ssbio/protein/sequence/utils/fasta.py | fasta_files_equal | def fasta_files_equal(seq_file1, seq_file2):
"""Check equality of a FASTA file to another FASTA file
Args:
seq_file1: Path to a FASTA file
seq_file2: Path to another FASTA file
Returns:
bool: If the sequences are the same
"""
# Load already set representative sequence
... | python | def fasta_files_equal(seq_file1, seq_file2):
"""Check equality of a FASTA file to another FASTA file
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seq_file1: Path to a FASTA file
seq_file2: Path to another FASTA file
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bool: If the sequences are the same
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SBRG/ssbio | ssbio/biopython/Bio/Struct/Protein.py | Protein.from_structure | def from_structure(cls, original, filter_residues):
"""
Loads structure as a protein, exposing
protein-specific methods.
"""
P = cls(original.id)
P.full_id = original.full_id
for child in original.child_dict.values():
copycat = deepcopy(child)... | python | def from_structure(cls, original, filter_residues):
"""
Loads structure as a protein, exposing
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"""
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SBRG/ssbio | ssbio/protein/sequence/properties/aggregation_propensity.py | AMYLPRED.get_aggregation_propensity | def get_aggregation_propensity(self, seq, outdir, cutoff_v=5, cutoff_n=5, run_amylmuts=False):
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Args:
seq (str, Seq, SeqRecord): Amino acid sequence
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seq (str, Seq, SeqRecord): Amino acid sequence
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SBRG/ssbio | ssbio/protein/sequence/properties/aggregation_propensity.py | AMYLPRED.run_amylpred2 | def run_amylpred2(self, seq, outdir, run_amylmuts=False):
"""Run all methods on the AMYLPRED2 web server for an amino acid sequence and gather results.
Result files are cached in ``/path/to/outdir/AMYLPRED2_results``.
Args:
seq (str): Amino acid sequence as a string
out... | python | def run_amylpred2(self, seq, outdir, run_amylmuts=False):
"""Run all methods on the AMYLPRED2 web server for an amino acid sequence and gather results.
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seq (str): Amino acid sequence as a string
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SBRG/ssbio | ssbio/protein/sequence/properties/aggregation_propensity.py | AMYLPRED.parse_method_results | def parse_method_results(self, results_file, met):
"""Parse the output of a AMYLPRED2 result file."""
result = str(open(results_file).read())
ind_s = str.find(result, 'HITS')
ind_e = str.find(result, '**NOTE')
tmp = result[ind_s + 10:ind_e].strip(" ")
hits_resid = []
... | python | def parse_method_results(self, results_file, met):
"""Parse the output of a AMYLPRED2 result file."""
result = str(open(results_file).read())
ind_s = str.find(result, 'HITS')
ind_e = str.find(result, '**NOTE')
tmp = result[ind_s + 10:ind_e].strip(" ")
hits_resid = []
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brycedrennan/eulerian-magnification | eulerian_magnification/io.py | _load_video | def _load_video(video_filename):
"""Load a video into a numpy array"""
video_filename = str(video_filename)
print("Loading " + video_filename)
if not os.path.isfile(video_filename):
raise Exception("File Not Found: %s" % video_filename)
# noinspection PyArgumentList
capture = cv2.VideoCa... | python | def _load_video(video_filename):
"""Load a video into a numpy array"""
video_filename = str(video_filename)
print("Loading " + video_filename)
if not os.path.isfile(video_filename):
raise Exception("File Not Found: %s" % video_filename)
# noinspection PyArgumentList
capture = cv2.VideoCa... | [
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brycedrennan/eulerian-magnification | eulerian_magnification/io.py | get_capture_dimensions | def get_capture_dimensions(capture):
"""Get the dimensions of a capture"""
width = int(capture.get(cv2.CAP_PROP_FRAME_WIDTH))
height = int(capture.get(cv2.CAP_PROP_FRAME_HEIGHT))
return width, height | python | def get_capture_dimensions(capture):
"""Get the dimensions of a capture"""
width = int(capture.get(cv2.CAP_PROP_FRAME_WIDTH))
height = int(capture.get(cv2.CAP_PROP_FRAME_HEIGHT))
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brycedrennan/eulerian-magnification | eulerian_magnification/io.py | save_video | def save_video(video, fps, save_filename='media/output.avi'):
"""Save a video to disk"""
# fourcc = cv2.CAP_PROP_FOURCC('M', 'J', 'P', 'G')
print(save_filename)
video = float_to_uint8(video)
fourcc = cv2.VideoWriter_fourcc(*'MJPG')
writer = cv2.VideoWriter(save_filename, fourcc, fps, (video.shap... | python | def save_video(video, fps, save_filename='media/output.avi'):
"""Save a video to disk"""
# fourcc = cv2.CAP_PROP_FOURCC('M', 'J', 'P', 'G')
print(save_filename)
video = float_to_uint8(video)
fourcc = cv2.VideoWriter_fourcc(*'MJPG')
writer = cv2.VideoWriter(save_filename, fourcc, fps, (video.shap... | [
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brycedrennan/eulerian-magnification | eulerian_magnification/base.py | show_frequencies | def show_frequencies(vid_data, fps, bounds=None):
"""Graph the average value of the video as well as the frequency strength"""
averages = []
if bounds:
for x in range(1, vid_data.shape[0] - 1):
averages.append(vid_data[x, bounds[2]:bounds[3], bounds[0]:bounds[1], :].sum())
else:
... | python | def show_frequencies(vid_data, fps, bounds=None):
"""Graph the average value of the video as well as the frequency strength"""
averages = []
if bounds:
for x in range(1, vid_data.shape[0] - 1):
averages.append(vid_data[x, bounds[2]:bounds[3], bounds[0]:bounds[1], :].sum())
else:
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brycedrennan/eulerian-magnification | eulerian_magnification/base.py | gaussian_video | def gaussian_video(video, shrink_multiple):
"""Create a gaussian representation of a video"""
vid_data = None
for x in range(0, video.shape[0]):
frame = video[x]
gauss_copy = np.ndarray(shape=frame.shape, dtype="float")
gauss_copy[:] = frame
for i in range(shrink_multiple):
... | python | def gaussian_video(video, shrink_multiple):
"""Create a gaussian representation of a video"""
vid_data = None
for x in range(0, video.shape[0]):
frame = video[x]
gauss_copy = np.ndarray(shape=frame.shape, dtype="float")
gauss_copy[:] = frame
for i in range(shrink_multiple):
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brycedrennan/eulerian-magnification | eulerian_magnification/base.py | combine_pyramid_and_save | def combine_pyramid_and_save(g_video, orig_video, enlarge_multiple, fps, save_filename='media/output.avi'):
"""Combine a gaussian video representation with the original and save to file"""
width, height = get_frame_dimensions(orig_video[0])
fourcc = cv2.VideoWriter_fourcc(*'MJPG')
print("Outputting to %... | python | def combine_pyramid_and_save(g_video, orig_video, enlarge_multiple, fps, save_filename='media/output.avi'):
"""Combine a gaussian video representation with the original and save to file"""
width, height = get_frame_dimensions(orig_video[0])
fourcc = cv2.VideoWriter_fourcc(*'MJPG')
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textmagic/textmagic-rest-python | textmagic/rest/models/messages.py | Messages.price | def price(self, from_=None, **kwargs):
"""
Check pricing for a new outbound message.
An useful synonym for "message" command with "dummy" parameters set to true.
:Example:
message = client.messages.price(from_="447624800500", phones="999000001", text="Hello!", lists="1909100")
... | python | def price(self, from_=None, **kwargs):
"""
Check pricing for a new outbound message.
An useful synonym for "message" command with "dummy" parameters set to true.
:Example:
message = client.messages.price(from_="447624800500", phones="999000001", text="Hello!", lists="1909100")
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message = client.messages.price(from_="447624800500", phones="999000001", text="Hello!", lists="1909100")
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textmagic/textmagic-rest-python | textmagic/rest/models/tokens.py | Tokens.refresh | def refresh(self):
"""
Refresh access token. Only non-expired tokens can be renewed.
:Example:
token = client.tokens.refresh()
"""
uri = "%s/%s" % (self.uri, "refresh")
response, instance = self.request("GET", uri)
return response.ok | python | def refresh(self):
"""
Refresh access token. Only non-expired tokens can be renewed.
:Example:
token = client.tokens.refresh()
"""
uri = "%s/%s" % (self.uri, "refresh")
response, instance = self.request("GET", uri)
return response.ok | [
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textmagic/textmagic-rest-python | textmagic/rest/models/user.py | Users.update | def update(self, **kwargs):
"""
Update an current User via a PUT request.
Returns True if success.
:Example:
client.user.update(firstName="John", lastName="Doe", company="TextMagic")
:param str firstName: User first name. Required.
:param str lastName: User la... | python | def update(self, **kwargs):
"""
Update an current User via a PUT request.
Returns True if success.
:Example:
client.user.update(firstName="John", lastName="Doe", company="TextMagic")
:param str firstName: User first name. Required.
:param str lastName: User la... | [
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Returns True if success.
:Example:
client.user.update(firstName="John", lastName="Doe", company="TextMagic")
:param str firstName: User first name. Required.
:param str lastName: User last name. Required.
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textmagic/textmagic-rest-python | textmagic/rest/models/user.py | Subaccounts.send_invite | def send_invite(self, **kwargs):
"""
Invite new subaccount.
Returns True if success.
:Example:
s = client.subaccounts.create(email="johndoe@yahoo.com", role="A")
:param str email: Subaccount email. Required.
:param str role: Subaccount role: `A` for administra... | python | def send_invite(self, **kwargs):
"""
Invite new subaccount.
Returns True if success.
:Example:
s = client.subaccounts.create(email="johndoe@yahoo.com", role="A")
:param str email: Subaccount email. Required.
:param str role: Subaccount role: `A` for administra... | [
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Returns True if success.
:Example:
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:param str email: Subaccount email. Required.
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textmagic/textmagic-rest-python | textmagic/rest/models/chats.py | Chats.by_phone | def by_phone(self, phone, **kwargs):
"""
Fetch messages from chat with specified phone number.
:Example:
chat = client.chats.by_phone(phone="447624800500")
:param str phone: Phone number in E.164 format.
:param int page: Fetch specified results page. Default=1
... | python | def by_phone(self, phone, **kwargs):
"""
Fetch messages from chat with specified phone number.
:Example:
chat = client.chats.by_phone(phone="447624800500")
:param str phone: Phone number in E.164 format.
:param int page: Fetch specified results page. Default=1
... | [
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textmagic/textmagic-rest-python | textmagic/rest/client.py | get_credentials | def get_credentials(env=None):
"""
Gets the TextMagic credentials from current environment
:param env: environment
:return: username, token
"""
environ = env or os.environ
try:
username = environ["TEXTMAGIC_USERNAME"]
token = environ["TEXTMAGIC_AUTH_TOKEN"]
return us... | python | def get_credentials(env=None):
"""
Gets the TextMagic credentials from current environment
:param env: environment
:return: username, token
"""
environ = env or os.environ
try:
username = environ["TEXTMAGIC_USERNAME"]
token = environ["TEXTMAGIC_AUTH_TOKEN"]
return us... | [
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textmagic/textmagic-rest-python | textmagic/rest/models/contacts.py | Lists.put_contacts | def put_contacts(self, uid, **kwargs):
"""
Assign contacts to the specified list.
:Example:
client.lists.put_contacts(uid=1901010, contacts="1723812,1239912")
:param int uid: The unique id of the List. Required.
:param str contacts: Contact ID(s), separated by com... | python | def put_contacts(self, uid, **kwargs):
"""
Assign contacts to the specified list.
:Example:
client.lists.put_contacts(uid=1901010, contacts="1723812,1239912")
:param int uid: The unique id of the List. Required.
:param str contacts: Contact ID(s), separated by com... | [
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:Example:
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:param int uid: The unique id of the List. Required.
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textmagic/textmagic-rest-python | textmagic/rest/models/contacts.py | Lists.delete_contacts | def delete_contacts(self, uid, **kwargs):
"""
Unassign contacts from the specified list.
If contacts assign only to the specified list, then delete permanently.
Returns True if success.
:Example:
client.lists.delete_contacts(uid=1901010, contacts="1723812,1239912")
... | python | def delete_contacts(self, uid, **kwargs):
"""
Unassign contacts from the specified list.
If contacts assign only to the specified list, then delete permanently.
Returns True if success.
:Example:
client.lists.delete_contacts(uid=1901010, contacts="1723812,1239912")
... | [
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textmagic/textmagic-rest-python | textmagic/rest/models/base.py | get_cert_file | def get_cert_file():
""" Get the certificates file for https"""
try:
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ca_cert_path = os.path.join(current_path, "..", "..", "..",
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return os.path.abspath(ca_cert_path)
except Exception:
... | python | def get_cert_file():
""" Get the certificates file for https"""
try:
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ca_cert_path = os.path.join(current_path, "..", "..", "..",
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return os.path.abspath(ca_cert_path)
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Update an Model via a PUT request
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"""
uri = "%s/%s" % (self.uri, uid)
response, instance = self.request("DELETE", uri)
return response.status == 204 | python | def delete_instance(self, uid):
"""
Delete an ObjectModel via a DELETE request
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response, instance = self.request("DELETE", uri)
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# We create the buffer every time instead of keeping the buffer (which is 32 bytes at least)
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI._unzip_file | def _unzip_file(self, src_path, dest_path, filename):
"""unzips file located at src_path into destination_path"""
self.logger.info("unzipping file...")
# construct full path (including file name) for unzipping
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.get_dataset_url | def get_dataset_url(self, tournament=1):
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tournament (int, optional): ID of the tournament, defaults to 1
Returns:
str: url of the current dataset
Example:
>>> NumerAPI().get_dataset_url()
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"""Fetch url of the current dataset.
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tournament (int, optional): ID of the tournament, defaults to 1
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.raw_query | def raw_query(self, query, variables=None, authorization=False):
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https://medium.com/numerai/getting-started-with-numerais-new-tournam... | python | def raw_query(self, query, variables=None, authorization=False):
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.get_staking_leaderboard | def get_staking_leaderboard(self, round_num=0, tournament=1):
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round.
Args:
round_num (int, optional): The round you are interested in,
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round_num (int, optional): The round you are interested in,
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.get_nmr_prize_pool | def get_nmr_prize_pool(self, round_num=0, tournament=1):
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Args:
round_num (int, optional): The round you are interested in,
defaults to current round.
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round_num (int, optional): The round you are interested in,
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.get_competitions | def get_competitions(self, tournament=1):
"""Retrieves information about all competitions
Args:
tournament (int, optional): ID of the tournament, defaults to 1
Returns:
list of dicts: list of rounds
Each round's dict contains the following items:
... | python | def get_competitions(self, tournament=1):
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Args:
tournament (int, optional): ID of the tournament, defaults to 1
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list of dicts: list of rounds
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.get_current_round | def get_current_round(self, tournament=1):
"""Get number of the current active round.
Args:
tournament (int): ID of the tournament (optional, defaults to 1)
Returns:
int: number of the current active round
Example:
>>> NumerAPI().get_current_round()... | python | def get_current_round(self, tournament=1):
"""Get number of the current active round.
Args:
tournament (int): ID of the tournament (optional, defaults to 1)
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int: number of the current active round
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.get_tournaments | def get_tournaments(self, only_active=True):
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only_active (bool): Flag to indicate of only active tournaments
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Returns:
list o... | python | def get_tournaments(self, only_active=True):
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only_active (bool): Flag to indicate of only active tournaments
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.get_submission_filenames | def get_submission_filenames(self, tournament=None, round_num=None):
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tournament (int): optionally filter by ID of the tournament
round_num (int): optionally filter round number
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tournament (int): optionally filter by ID of the tournament
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.get_rankings | def get_rankings(self, limit=50, offset=0):
"""Get the overall ranking
Args:
limit (int): number of items to return (optional, defaults to 50)
offset (int): number of items to skip (optional, defaults to 0)
Returns:
list of dicts: list of ranking items
... | python | def get_rankings(self, limit=50, offset=0):
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limit (int): number of items to return (optional, defaults to 50)
offset (int): number of items to skip (optional, defaults to 0)
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.get_submission_ids | def get_submission_ids(self, tournament=1):
"""Get dict with username->submission_id mapping.
Args:
tournament (int): ID of the tournament (optional, defaults to 1)
Returns:
dict: username->submission_id mapping, string->string
Example:
>>> NumerAPI... | python | def get_submission_ids(self, tournament=1):
"""Get dict with username->submission_id mapping.
Args:
tournament (int): ID of the tournament (optional, defaults to 1)
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dict: username->submission_id mapping, string->string
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"""Get all information about you!
Returns:
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* availableUsd (`decimal.Decimal`)
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.get_transactions | def get_transactions(self):
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Returns:
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* nmrDeposits (`list`) contains items with fields:
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"""Get all your deposits and withdrawals.
Returns:
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.get_stakes | def get_stakes(self):
"""List all your stakes.
Returns:
list of dicts: stakes
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* confidence (`decimal.Decimal`)
* roundNumber (`int`)
* tournamentId (`int`)
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Returns:
list of dicts: stakes
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.submission_status | def submission_status(self, submission_id=None):
"""submission status of the last submission associated with the account.
Args:
submission_id (str): submission of interest, defaults to the last
submission done with the account
Returns:
dict: submission s... | python | def submission_status(self, submission_id=None):
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submission_id (str): submission of interest, defaults to the last
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.upload_predictions | def upload_predictions(self, file_path, tournament=1):
"""Upload predictions from file.
Args:
file_path (str): CSV file with predictions that will get uploaded
tournament (int): ID of the tournament (optional, defaults to 1)
Returns:
str: submission_id
... | python | def upload_predictions(self, file_path, tournament=1):
"""Upload predictions from file.
Args:
file_path (str): CSV file with predictions that will get uploaded
tournament (int): ID of the tournament (optional, defaults to 1)
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str: submission_id
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.check_submission_successful | def check_submission_successful(self, submission_id=None):
"""Check if the last submission passes submission criteria.
Args:
submission_id (str, optional): submission of interest, defaults to
the last submission done with the account
Return:
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.tournament_number2name | def tournament_number2name(self, number):
"""Translate tournament number to tournament name.
Args:
number (int): tournament number to translate
Returns:
name (str): name of the tournament or `None` if unknown.
Examples:
>>> NumerAPI().tournament_num... | python | def tournament_number2name(self, number):
"""Translate tournament number to tournament name.
Args:
number (int): tournament number to translate
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uuazed/numerapi | numerapi/numerapi.py | NumerAPI.tournament_name2number | def tournament_name2number(self, name):
"""Translate tournament name to tournament number.
Args:
name (str): tournament name to translate
Returns:
number (int): number of the tournament or `None` if unknown.
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>>> NumerAPI().tournament_name2... | python | def tournament_name2number(self, name):
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name (str): tournament name to translate
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uuazed/numerapi | numerapi/cli.py | staking_leaderboard | def staking_leaderboard(round_num=0, tournament=1):
"""Retrieves the staking competition leaderboard for the given round."""
click.echo(prettify(napi.get_staking_leaderboard(tournament=tournament,
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uuazed/numerapi | numerapi/cli.py | rankings | def rankings(limit=20, offset=0):
"""Get the overall rankings."""
click.echo(prettify(napi.get_rankings(limit=limit, offset=offset))) | python | def rankings(limit=20, offset=0):
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uuazed/numerapi | numerapi/cli.py | submission_filenames | def submission_filenames(round_num=None, tournament=None):
"""Get filenames of your submissions"""
click.echo(prettify(
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"""Get filenames of your submissions"""
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kirbs-/hide_code | hide_code/hide_code.py | install_bootstrapped_files | def install_bootstrapped_files(nb_path=None, server_config=True, DEBUG=False):
"""
Installs javascript and exporting server extensions in Jupyter notebook.
Args:
nb_path (string): Path to notebook module.
server_config (boolean): Install exporting server extensions.
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nb_path (string): Path to notebook module.
server_config (boolean): Install exporting server extensions.
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kirbs-/hide_code | hide_code/hide_code.py | ipynb_file_name | def ipynb_file_name(params):
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pytroll/pyspectral | pyspectral/radiance_tb_conversion.py | radiance2tb | def radiance2tb(rad, wavelength):
"""
Get the Tb from the radiance using the Planck function
rad:
Radiance in SI units
wavelength:
Wavelength in SI units (meter)
"""
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return rad2temp(wavelength, rad) | python | def radiance2tb(rad, wavelength):
"""
Get the Tb from the radiance using the Planck function
rad:
Radiance in SI units
wavelength:
Wavelength in SI units (meter)
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"rad",
")"
] | Get the Tb from the radiance using the Planck function
rad:
Radiance in SI units
wavelength:
Wavelength in SI units (meter) | [
"Get",
"the",
"Tb",
"from",
"the",
"radiance",
"using",
"the",
"Planck",
"function"
] | fd296c0e0bdf5364fa180134a1292665d6bc50a3 | https://github.com/pytroll/pyspectral/blob/fd296c0e0bdf5364fa180134a1292665d6bc50a3/pyspectral/radiance_tb_conversion.py#L249-L259 | train |
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