idx int64 0 251k | question stringlengths 53 3.53k | target stringlengths 5 1.23k | len_question int64 20 893 | len_target int64 3 238 |
|---|---|---|---|---|
1,400 | def make_timestamp ( el_time ) : # Calc hours hrs = el_time // 3600.0 # Calc minutes mins = ( el_time % 3600.0 ) // 60.0 # Calc seconds secs = el_time % 60.0 # Construct timestamp string stamp = "{0}h {1}m {2}s" . format ( int ( hrs ) , int ( mins ) , int ( secs ) ) # Return return stamp | Generate an hour - minutes - seconds timestamp from an interval in seconds . | 101 | 15 |
1,401 | def check_geom ( c1 , a1 , c2 , a2 , tol = _DEF . XYZ_COORD_MATCH_TOL ) : # Import(s) from . . const import atom_num import numpy as np from . . const import EnumCheckGeomMismatch as ECGM # Initialize return value to success condition match = True #** Check coords for suitable shape. Assume 1-D np.arrays. if not len ( ... | Check for consistency of two geometries and atom symbol lists | 818 | 12 |
1,402 | def template_subst ( template , subs , delims = ( '<' , '>' ) ) : # Store the template into the working variable subst_text = template # Iterate over subs and perform the .replace() calls for ( k , v ) in subs . items ( ) : subst_text = subst_text . replace ( delims [ 0 ] + k + delims [ 1 ] , v ) ## next tup # Return t... | Perform substitution of content into tagged string . | 100 | 9 |
1,403 | def assert_npfloatarray ( obj , varname , desc , exc , tc , errsrc ) : # Imports import numpy as np # Check for whether member or object is to be checked if varname is None : var = obj else : # Try to get the variable to be typechecked try : var = getattr ( obj , varname ) except AttributeError : raise exc ( tc , "Attr... | Assert a value is an |nparray| of NumPy floats . | 285 | 16 |
1,404 | def advance ( self ) : elem = next ( self . _iterable ) for deque in self . _deques : deque . append ( elem ) | Advance the base iterator publish to constituent iterators . | 35 | 11 |
1,405 | def _advance_pattern_generators ( self , p ) : valid_generators = [ ] for g in p . generators : for trial in range ( self . max_trials ) : # Generate a new position and add generator if it's ok if np . alltrue ( [ self . __distance_valid ( g , v , p ) for v in valid_generators ] ) : valid_generators . append ( g ) brea... | Advance the parameters for each generator for this presentation . | 154 | 11 |
1,406 | def _advance_params ( self ) : for p in [ 'x' , 'y' , 'direction' ] : self . force_new_dynamic_value ( p ) self . last_time = self . time_fn ( ) | Explicitly generate new values for these parameters only when appropriate . | 53 | 13 |
1,407 | def register ( self , settings_class = NoSwitcher , * simple_checks , * * conditions ) : if settings_class is NoSwitcher : def decorator ( cls ) : self . register ( cls , * simple_checks , * * conditions ) return cls return decorator available_checks = self . checks . keys ( ) for condition in conditions . keys ( ) : i... | Register a settings class with the switcher . Can be passed the settings class to register or be used as a decorator . | 128 | 25 |
1,408 | def _peek_buffer ( self , i = 0 ) : while len ( self . _buffer ) <= i : self . _buffer . append ( next ( self . _source ) ) return self . _buffer [ i ] | Get the next line without consuming it . | 48 | 8 |
1,409 | def _make_readline_peeker ( self ) : counter = itertools . count ( 0 ) def readline ( ) : try : return self . _peek_buffer ( next ( counter ) ) except StopIteration : return '' return readline | Make a readline - like function which peeks into the source . | 55 | 14 |
1,410 | def _add_node ( self , node , depth ) : self . _topmost_node . add_child ( node , bool ( depth [ 1 ] ) ) self . _stack . append ( ( depth , node ) ) | Add a node to the graph and the stack . | 48 | 10 |
1,411 | def _load_data ( self , atom_syms , coords , bohrs = True ) : # Imports import numpy as np from . const import atom_num , PHYS from . error import XYZError # Gripe if already initialized if 'geoms' in dir ( self ) : raise XYZError ( XYZError . OVERWRITE , "Cannot overwrite contents of existing OpanXYZ" , "" ) ## end if... | Internal function for making XYZ object from explicit geom data . | 529 | 13 |
1,412 | def geom_iter ( self , g_nums ) : # Using the custom coded pack_tups to not have to care whether the # input is iterable from . utils import pack_tups vals = pack_tups ( g_nums ) for val in vals : yield self . geom_single ( val [ 0 ] ) | Iterator over a subset of geometries . | 76 | 9 |
1,413 | def dist_single ( self , g_num , at_1 , at_2 ) : # Import used math library function(s) import numpy as np from scipy import linalg as spla from . utils import safe_cast as scast # The below errors are explicitly thrown since values are multiplied by # three when they are used as an index and thus give non-intuitive # ... | Distance between two atoms . | 383 | 5 |
1,414 | def dist_iter ( self , g_nums , ats_1 , ats_2 , invalid_error = False ) : # Imports import numpy as np from . utils import pack_tups # Print the function inputs if debug mode is on if _DEBUG : # pragma: no cover print ( "g_nums = {0}" . format ( g_nums ) ) print ( "ats_1 = {0}" . format ( ats_1 ) ) print ( "ats_2 = {0}... | Iterator over selected interatomic distances . | 268 | 7 |
1,415 | def angle_single ( self , g_num , at_1 , at_2 , at_3 ) : # Imports import numpy as np from . utils import safe_cast as scast from . utils . vector import vec_angle # The below errors are explicitly thrown since they are multiplied by # three when they are used as an index and thus give non-intuitive # errors in later c... | Spanning angle among three atoms . | 702 | 8 |
1,416 | def angle_iter ( self , g_nums , ats_1 , ats_2 , ats_3 , invalid_error = False ) : # Suitability of ats_n indices will be checked within the # self.angle_single() calls and thus no check is needed here. # Import the tuple-generating function from . utils import pack_tups # Print the function inputs if debug mode is on ... | Iterator over selected atomic angles . | 323 | 6 |
1,417 | def dihed_iter ( self , g_nums , ats_1 , ats_2 , ats_3 , ats_4 , invalid_error = False ) : # Suitability of ats_n indices will be checked within the # self.dihed_single() calls and thus no check is needed here. # Import the tuple-generating function from . utils import pack_tups # Print the function inputs if debug mod... | Iterator over selected dihedral angles . | 337 | 7 |
1,418 | def displ_single ( self , g_num , at_1 , at_2 ) : # Library imports import numpy as np from . utils import safe_cast as scast # The below errors are explicitly thrown since they are multiplied by # three when they are used as an index and thus give non-intuitive # errors. # Complain if at_1 is invalid if not ( - self .... | Displacement vector between two atoms . | 428 | 8 |
1,419 | def displ_iter ( self , g_nums , ats_1 , ats_2 , invalid_error = False ) : # Import the tuple-generating function from . utils import pack_tups # Print the function inputs if debug mode is on if _DEBUG : # pragma: no cover print ( "g_nums = {0}" . format ( g_nums ) ) print ( "ats_1 = {0}" . format ( ats_1 ) ) print ( "... | Iterator over indicated displacement vectors . | 246 | 6 |
1,420 | def _none_subst ( self , * args ) : # Imports import numpy as np # Initialize argument list return value, and as None not found arglist = [ a for a in args ] none_found = False # Check for None values none_vals = list ( map ( lambda e : isinstance ( e , type ( None ) ) , arglist ) ) # Error if more than one None; handl... | Helper function to insert full ranges for |None| for X_iter methods . | 354 | 16 |
1,421 | def guess_external_url ( local_host , port ) : if local_host in [ '0.0.0.0' , '::' ] : # The server is listening on all interfaces, but we have to pick one. # The system's FQDN should give us a hint. local_host = socket . getfqdn ( ) # https://github.com/vfaronov/turq/issues/9 match = IPV4_REVERSE_DNS . match ( local_h... | Return a URL that is most likely to route to local_host from outside . | 333 | 16 |
1,422 | def _check_column_lengths ( self ) : column_lengths_dict = { name : len ( xs ) for ( name , xs ) in self . columns_dict . items ( ) } unique_column_lengths = set ( column_lengths_dict . values ( ) ) if len ( unique_column_lengths ) != 1 : raise ValueError ( "Mismatch between lengths of columns: %s" % ( column_lengths_d... | Make sure columns are of the same length or else DataFrame construction will fail . | 105 | 16 |
1,423 | def new_from_files ( self , basepath , basename , repo , bohrs = False , software = _E_SW . ORCA , repo_clobber = False , * * kwargs ) : # Imports import os from os import path as osp from . . xyz import OpanXYZ as OX from . . grad import OrcaEngrad as OE from . . hess import OrcaHess as OH from . repo import OpanAnhar... | Initialize with data from files . | 751 | 7 |
1,424 | def remote_exception ( exc , tb ) : if type ( exc ) in exceptions : typ = exceptions [ type ( exc ) ] return typ ( exc , tb ) else : try : typ = type ( exc . __class__ . __name__ , ( RemoteException , type ( exc ) ) , { 'exception_type' : type ( exc ) } ) exceptions [ type ( exc ) ] = typ return typ ( exc , tb ) except... | Metaclass that wraps exception type in RemoteException | 102 | 10 |
1,425 | def reads_overlapping_variants ( variants , samfile , * * kwargs ) : chromosome_names = set ( samfile . references ) for variant in variants : # I imagine the conversation went like this: # A: "Hey, I have an awesome idea" # B: "What's up?" # A: "Let's make two nearly identical reference genomes" # B: "But...that sound... | Generates sequence of tuples each containing a variant paired with a list of AlleleRead objects . | 250 | 21 |
1,426 | def group_reads_by_allele ( allele_reads ) : allele_to_reads_dict = defaultdict ( list ) for allele_read in allele_reads : allele_to_reads_dict [ allele_read . allele ] . append ( allele_read ) return allele_to_reads_dict | Returns dictionary mapping each allele s nucleotide sequence to a list of supporting AlleleRead objects . | 66 | 20 |
1,427 | def from_locus_read ( cls , locus_read , n_ref ) : sequence = locus_read . sequence reference_positions = locus_read . reference_positions # positions of the nucleotides before and after the variant within # the read sequence read_pos_before = locus_read . base0_read_position_before_variant read_pos_after = locus_read ... | Given a single LocusRead object return either an AlleleRead or None | 663 | 16 |
1,428 | def most_common_nucleotides ( partitioned_read_sequences ) : counts , variant_column_indices = nucleotide_counts ( partitioned_read_sequences ) max_count_per_column = counts . max ( axis = 0 ) assert len ( max_count_per_column ) == counts . shape [ 1 ] max_nucleotide_index_per_column = np . argmax ( counts , axis = 0 )... | Find the most common nucleotide at each offset to the left and right of a variant . | 207 | 18 |
1,429 | def point_displ ( pt1 , pt2 ) : #Imports import numpy as np # Make iterable if not np . iterable ( pt1 ) : pt1 = np . float64 ( np . array ( [ pt1 ] ) ) else : pt1 = np . float64 ( np . array ( pt1 ) . squeeze ( ) ) ## end if if not np . iterable ( pt2 ) : pt2 = np . float64 ( np . array ( [ pt2 ] ) ) else : pt2 = np .... | Calculate the displacement vector between two n - D points . | 168 | 13 |
1,430 | def point_dist ( pt1 , pt2 ) : # Imports from scipy import linalg as spla dist = spla . norm ( point_displ ( pt1 , pt2 ) ) return dist | Calculate the Euclidean distance between two n - D points . | 47 | 15 |
1,431 | def point_rotate ( pt , ax , theta ) : # Imports import numpy as np # Ensure pt is reducible to 3-D vector. pt = make_nd_vec ( pt , nd = 3 , t = np . float64 , norm = False ) # Calculate the rotation rot_pt = np . dot ( mtx_rot ( ax , theta , reps = 1 ) , pt ) # Should be ready to return return rot_pt | Rotate a 3 - D point around a 3 - D axis through the origin . | 100 | 17 |
1,432 | def point_reflect ( pt , nv ) : # Imports import numpy as np from scipy import linalg as spla # Ensure pt is reducible to 3-D vector pt = make_nd_vec ( pt , nd = 3 , t = np . float64 , norm = False ) # Transform the point and return refl_pt = np . dot ( mtx_refl ( nv , reps = 1 ) , pt ) return refl_pt | Reflect a 3 - D point through a plane intersecting the origin . | 103 | 15 |
1,433 | def geom_reflect ( g , nv ) : # Imports import numpy as np # Force g to n-vector g = make_nd_vec ( g , nd = None , t = np . float64 , norm = False ) # Transform the geometry and return refl_g = np . dot ( mtx_refl ( nv , reps = ( g . shape [ 0 ] // 3 ) ) , g ) . reshape ( ( g . shape [ 0 ] , 1 ) ) return refl_g | Reflection symmetry operation . | 113 | 5 |
1,434 | def geom_rotate ( g , ax , theta ) : # Imports import numpy as np # Force g to n-vector g = make_nd_vec ( g , nd = None , t = np . float64 , norm = False ) # Perform rotation and return rot_g = np . dot ( mtx_rot ( ax , theta , reps = ( g . shape [ 0 ] // 3 ) ) , g ) . reshape ( ( g . shape [ 0 ] , 1 ) ) return rot_g | Rotation symmetry operation . | 114 | 5 |
1,435 | def symm_op ( g , ax , theta , do_refl ) : # Imports import numpy as np # Depend on lower functions' geometry vector coercion. Just # do the rotation and, if indicated, the reflection. gx = geom_rotate ( g , ax , theta ) if do_refl : gx = geom_reflect ( gx , ax ) ## end if # Should be good to go return gx | Perform general point symmetry operation on a geometry . | 96 | 10 |
1,436 | def geom_find_rotsymm ( g , atwts , ax , improp , nmax = _DEF . SYMM_MATCH_NMAX , tol = _DEF . SYMM_MATCH_TOL ) : # Imports import numpy as np # Vectorize the geometry g = make_nd_vec ( g , nd = None , t = np . float64 , norm = False ) # Ensure a 3-D axis vector ax = make_nd_vec ( ax , nd = 3 , t = np . float64 , norm ... | Identify highest - order symmetry for a geometry on a given axis . | 279 | 14 |
1,437 | def g_subset ( g , atwts , atwt , digits = _DEF . SYMM_ATWT_ROUND_DIGITS ) : # Imports import numpy as np # Ensure g and atwts are n-D vectors g = make_nd_vec ( g , nd = None , t = np . float64 , norm = False ) atwts = make_nd_vec ( atwts , nd = None , t = np . float64 , norm = False ) # Ensure dims match (should alrea... | Extract a subset of a geometry matching a desired atom . | 309 | 12 |
1,438 | def mtx_refl ( nv , reps = 1 ) : # Imports import numpy as np from scipy import linalg as spla from . . const import PRM # Ensure |nv| is large enough for confident directionality if spla . norm ( nv ) < PRM . ZERO_VEC_TOL : raise ValueError ( "Norm of 'nv' is too small." ) ## end if # Ensure nv is a normalized np.floa... | Generate block - diagonal reflection matrix about nv . | 412 | 11 |
1,439 | def mtx_rot ( ax , theta , reps = 1 ) : # Imports import numpy as np from scipy import linalg as spla from . . const import PRM # Ensure |ax| is large enough for confident directionality if spla . norm ( ax ) < PRM . ZERO_VEC_TOL : raise ValueError ( "Norm of 'ax' is too small." ) ## end if # Ensure ax is a normalized ... | Generate block - diagonal rotation matrix about ax . | 504 | 10 |
1,440 | def ff ( items , targets ) : bins = [ ( target , [ ] ) for target in targets ] skip = [ ] for item in items : for target , content in bins : if item <= ( target - sum ( content ) ) : content . append ( item ) break else : skip . append ( item ) return bins , skip | First - Fit | 69 | 3 |
1,441 | def ffd ( items , targets , * * kwargs ) : sizes = zip ( items , weight ( items , * * kwargs ) ) sizes = sorted ( sizes , key = operator . itemgetter ( 1 ) , reverse = True ) items = map ( operator . itemgetter ( 0 ) , sizes ) return ff ( items , targets ) | First - Fit Decreasing | 75 | 5 |
1,442 | def mr ( items , targets , * * kwargs ) : bins = [ ( target , [ ] ) for target in targets ] skip = [ ] for item in items : capacities = [ target - sum ( content ) for target , content in bins ] weighted = weight ( capacities , * * kwargs ) ( target , content ) , capacity , _ = max ( zip ( bins , capacities , weighted )... | Max - Rest | 121 | 3 |
1,443 | def bf ( items , targets , * * kwargs ) : bins = [ ( target , [ ] ) for target in targets ] skip = [ ] for item in items : containers = [ ] capacities = [ ] for target , content in bins : capacity = target - sum ( content ) if item <= capacity : containers . append ( content ) capacities . append ( capacity - item ) if... | Best - Fit | 140 | 3 |
1,444 | def bfd ( items , targets , * * kwargs ) : sizes = zip ( items , weight ( items , * * kwargs ) ) sizes = sorted ( sizes , key = operator . itemgetter ( 1 ) , reverse = True ) items = map ( operator . itemgetter ( 0 ) , sizes ) return bf ( items , targets , * * kwargs ) | Best - Fit Decreasing | 82 | 5 |
1,445 | def trim_sequences ( variant_sequence , reference_context ) : cdna_prefix = variant_sequence . prefix cdna_alt = variant_sequence . alt cdna_suffix = variant_sequence . suffix # if the transcript is on the reverse strand then we have to # take the sequence PREFIX|VARIANT|SUFFIX # and take the complement of XIFFUS|TNAIR... | A VariantSequence and ReferenceContext may contain a different number of nucleotides before the variant locus . Furthermore the VariantSequence is always expressed in terms of the positive strand against which it aligned but reference transcripts may have sequences from the negative strand of the genome . Take the reve... | 494 | 88 |
1,446 | def count_mismatches_before_variant ( reference_prefix , cdna_prefix ) : if len ( reference_prefix ) != len ( cdna_prefix ) : raise ValueError ( "Expected reference prefix '%s' to be same length as %s" % ( reference_prefix , cdna_prefix ) ) return sum ( xi != yi for ( xi , yi ) in zip ( reference_prefix , cdna_prefix )... | Computes the number of mismatching nucleotides between two cDNA sequences before a variant locus . | 100 | 21 |
1,447 | def count_mismatches_after_variant ( reference_suffix , cdna_suffix ) : len_diff = len ( cdna_suffix ) - len ( reference_suffix ) # if the reference is shorter than the read, the read runs into the intron - these count as # mismatches return sum ( xi != yi for ( xi , yi ) in zip ( reference_suffix , cdna_suffix ) ) + m... | Computes the number of mismatching nucleotides between two cDNA sequences after a variant locus . | 108 | 21 |
1,448 | def compute_offset_to_first_complete_codon ( offset_to_first_complete_reference_codon , n_trimmed_from_reference_sequence ) : if n_trimmed_from_reference_sequence <= offset_to_first_complete_reference_codon : return ( offset_to_first_complete_reference_codon - n_trimmed_from_reference_sequence ) else : n_nucleotides_tr... | Once we ve aligned the variant sequence to the ReferenceContext we need to transfer reading frame from the reference transcripts to the variant sequences . | 168 | 26 |
1,449 | def match_variant_sequence_to_reference_context ( variant_sequence , reference_context , min_transcript_prefix_length , max_transcript_mismatches , include_mismatches_after_variant = False , max_trimming_attempts = 2 ) : variant_sequence_in_reading_frame = None # if we can't get the variant sequence to match this refer... | Iteratively trim low - coverage subsequences of a variant sequence until it either matches the given reference context or there are too few nucleotides left in the variant sequence . | 706 | 34 |
1,450 | def _check_codons ( self ) : for stop_codon in self . stop_codons : if stop_codon in self . codon_table : if self . codon_table [ stop_codon ] != "*" : raise ValueError ( ( "Codon '%s' not found in stop_codons, but codon table " "indicates that it should be" ) % ( stop_codon , ) ) else : self . codon_table [ stop_codon... | If codon table is missing stop codons then add them . | 282 | 13 |
1,451 | def copy ( self , name , start_codons = None , stop_codons = None , codon_table = None , codon_table_changes = None ) : new_start_codons = ( self . start_codons . copy ( ) if start_codons is None else start_codons ) new_stop_codons = ( self . stop_codons . copy ( ) if stop_codons is None else stop_codons ) new_codon_ta... | Make copy of this GeneticCode object with optional replacement values for all fields . | 202 | 15 |
1,452 | def start ( self ) : self . running = True self . thread = threading . Thread ( target = self . _main_loop ) self . thread . start ( ) | Start listening to changes | 36 | 4 |
1,453 | def subscribe ( self , field_names ) : available_controls = dict ( self . raildriver . get_controller_list ( ) ) . values ( ) for field in field_names : if field not in available_controls : raise ValueError ( 'Cannot subscribe to a missing controller {}' . format ( field ) ) self . subscribed_fields = field_names | Subscribe to given fields . | 80 | 5 |
1,454 | def set_matrix_dimensions ( self , bounds , xdensity , ydensity ) : self . bounds = bounds self . xdensity = xdensity self . ydensity = ydensity scs = SheetCoordinateSystem ( bounds , xdensity , ydensity ) for of in self . output_fns : if isinstance ( of , TransferFn ) : of . initialize ( SCS = scs , shape = scs . shap... | Change the dimensions of the matrix into which the pattern will be drawn . Users of this class should call this method rather than changing the bounds xdensity and ydensity parameters directly . Subclasses can override this method to update any internal data structures that may depend on the matrix dimensions . | 93 | 55 |
1,455 | def state_push ( self ) : for of in self . output_fns : if hasattr ( of , 'state_push' ) : of . state_push ( ) super ( PatternGenerator , self ) . state_push ( ) | Save the state of the output functions to be restored with state_pop . | 52 | 15 |
1,456 | def state_pop ( self ) : for of in self . output_fns : if hasattr ( of , 'state_pop' ) : of . state_pop ( ) super ( PatternGenerator , self ) . state_pop ( ) | Restore the state of the output functions saved by state_push . | 52 | 14 |
1,457 | def pil ( self , * * params_to_override ) : from PIL . Image import fromarray nchans = self . num_channels ( ) if nchans in [ 0 , 1 ] : mode , arr = None , self ( * * params_to_override ) arr = ( 255.0 / arr . max ( ) * ( arr - arr . min ( ) ) ) . astype ( np . uint8 ) elif nchans in [ 3 , 4 ] : mode = 'RGB' if nchans ... | Returns a PIL image for this pattern overriding parameters if provided . | 192 | 13 |
1,458 | def state_push ( self ) : super ( Composite , self ) . state_push ( ) for gen in self . generators : gen . state_push ( ) | Push the state of all generators | 34 | 6 |
1,459 | def state_pop ( self ) : super ( Composite , self ) . state_pop ( ) for gen in self . generators : gen . state_pop ( ) | Pop the state of all generators | 34 | 6 |
1,460 | def function ( self , p ) : generators = self . _advance_pattern_generators ( p ) assert hasattr ( p . operator , 'reduce' ) , repr ( p . operator ) + " does not support 'reduce'." # CEBALERT: mask gets applied by all PGs including the Composite itself # (leads to redundant calculations in current lissom_oo_or usage, b... | Constructs combined pattern out of the individual ones . | 250 | 10 |
1,461 | def compile_column ( name : str , data_type : str , nullable : bool ) -> str : null_str = 'NULL' if nullable else 'NOT NULL' return '{name} {data_type} {null},' . format ( name = name , data_type = data_type , null = null_str ) | Create column definition statement . | 73 | 5 |
1,462 | def create ( self , no_data = False ) : if self . query : ddl_statement = self . compile_create_as ( ) else : ddl_statement = self . compile_create ( ) if no_data : ddl_statement += '\nWITH NO DATA' return ddl_statement , self . query_values | Declare materalized view . | 74 | 7 |
1,463 | def predicted_effects_for_variant ( variant , transcript_id_whitelist = None , only_coding_changes = True ) : effects = [ ] for transcript in variant . transcripts : if only_coding_changes and not transcript . complete : logger . info ( "Skipping transcript %s for variant %s because it's incomplete" , transcript . name... | For a given variant return its set of predicted effects . Optionally filter to transcripts where this variant results in a non - synonymous change to the protein sequence . | 367 | 31 |
1,464 | def reference_transcripts_for_variant ( variant , transcript_id_whitelist = None , only_coding_changes = True ) : predicted_effects = predicted_effects_for_variant ( variant = variant , transcript_id_whitelist = transcript_id_whitelist , only_coding_changes = only_coding_changes ) return [ effect . transcript for effec... | For a given variant find all the transcripts which overlap the variant and for which it has a predictable effect on the amino acid sequence of the protein . | 93 | 29 |
1,465 | def pileup_reads_at_position ( samfile , chromosome , base0_position ) : # TODO: I want to pass truncate=True, stepper="all" # but for some reason I get this error: # pileup() got an unexpected keyword argument 'truncate' # ...even though these options are listed in the docs for pysam 0.9.0 # for column in samfile . pi... | Returns a pileup column at the specified position . Unclear if a function like this is hiding somewhere in pysam API . | 167 | 26 |
1,466 | def locus_read_generator ( samfile , chromosome , base1_position_before_variant , base1_position_after_variant , use_duplicate_reads = USE_DUPLICATE_READS , use_secondary_alignments = USE_SECONDARY_ALIGNMENTS , min_mapping_quality = MIN_READ_MAPPING_QUALITY ) : logger . debug ( "Gathering reads at locus %s: %d-%d" , ch... | Generator that yields a sequence of ReadAtLocus records for reads which contain the positions before and after a variant . The actual work to figure out if what s between those positions matches a variant happens later in the variant_reads module . | 444 | 48 |
1,467 | def locus_reads_dataframe ( * args , * * kwargs ) : df_builder = DataFrameBuilder ( LocusRead , variant_columns = False , converters = { "reference_positions" : list_to_string , "quality_scores" : list_to_string , } ) for locus_read in locus_read_generator ( * args , * * kwargs ) : df_builder . add ( variant = None , e... | Traverse a BAM file to find all the reads overlapping a specified locus . | 122 | 17 |
1,468 | def copy_from_csv_sql ( qualified_name : str , delimiter = ',' , encoding = 'utf8' , null_str = '' , header = True , escape_str = '\\' , quote_char = '"' , force_not_null = None , force_null = None ) : options = [ ] options . append ( "DELIMITER '%s'" % delimiter ) options . append ( "NULL '%s'" % null_str ) if header ... | Generate copy from csv statement . | 268 | 8 |
1,469 | def sort_protein_sequences ( protein_sequences ) : return list ( sorted ( protein_sequences , key = ProteinSequence . ascending_sort_key , reverse = True ) ) | Sort protein sequences in decreasing order of priority | 41 | 8 |
1,470 | def reads_generator_to_protein_sequences_generator ( variant_and_overlapping_reads_generator , transcript_id_whitelist = None , protein_sequence_length = PROTEIN_SEQUENCE_LENGTH , min_alt_rna_reads = MIN_ALT_RNA_READS , min_variant_sequence_coverage = MIN_VARIANT_SEQUENCE_COVERAGE , min_transcript_prefix_length = MIN_T... | Translates each coding variant in a collection to one or more Translation objects which are then aggregated into equivalent ProteinSequence objects . | 867 | 27 |
1,471 | def from_translation_key ( cls , translation_key , translations , overlapping_reads , ref_reads , alt_reads , alt_reads_supporting_protein_sequence , transcripts_overlapping_variant , transcripts_supporting_protein_sequence , gene ) : return cls ( amino_acids = translation_key . amino_acids , variant_aa_interval_start ... | Create a ProteinSequence object from a TranslationKey along with all the extra fields a ProteinSequence requires . | 250 | 22 |
1,472 | def make_delete_table ( table : Table , delete_prefix = 'delete_from__' ) -> Table : name = delete_prefix + table . name primary_key = table . primary_key key_names = set ( primary_key . column_names ) columns = [ column for column in table . columns if column . name in key_names ] table = Table ( name , columns , prim... | Table referencing a delete from using primary key join . | 90 | 10 |
1,473 | def trim_variant_fields ( location , ref , alt ) : if len ( alt ) > 0 and ref . startswith ( alt ) : # if alt is a prefix of the ref sequence then we actually have a # deletion like: # g.10 GTT > GT # which can be trimmed to # g.12 'T'>'' ref = ref [ len ( alt ) : ] location += len ( alt ) alt = "" if len ( ref ) > 0 a... | Trims common prefixes from the ref and alt sequences | 199 | 11 |
1,474 | def base0_interval_for_variant ( variant ) : base1_location , ref , alt = trim_variant ( variant ) return base0_interval_for_variant_fields ( base1_location = base1_location , ref = ref , alt = alt ) | Inteval of interbase offsets of the affected reference positions for a particular variant . | 63 | 16 |
1,475 | def interbase_range_affected_by_variant_on_transcript ( variant , transcript ) : if variant . is_insertion : if transcript . strand == "+" : # base-1 position of an insertion is the genomic nucleotide # before any inserted mutant nucleotides, so the start offset # of the actual inserted nucleotides is one past that ref... | Convert from a variant s position in global genomic coordinates on the forward strand to an interval of interbase offsets on a particular transcript s mRNA . | 354 | 29 |
1,476 | def insert ( conn , qualified_name : str , column_names , records ) : query = create_insert_statement ( qualified_name , column_names ) with conn : with conn . cursor ( cursor_factory = NamedTupleCursor ) as cursor : for record in records : cursor . execute ( query , record ) | Insert a collection of namedtuple records . | 69 | 9 |
1,477 | def insert_many ( conn , tablename , column_names , records , chunksize = 2500 ) : groups = chunks ( records , chunksize ) column_str = ',' . join ( column_names ) insert_template = 'INSERT INTO {table} ({columns}) VALUES {values}' . format ( table = tablename , columns = column_str , values = '{0}' ) with conn : with ... | Insert many records by chunking data into insert statements . | 169 | 11 |
1,478 | def upsert_records ( conn , records , upsert_statement ) : with conn : with conn . cursor ( ) as cursor : for record in records : cursor . execute ( upsert_statement , record ) | Upsert records . | 45 | 5 |
1,479 | def delete_joined_table_sql ( qualified_name , removing_qualified_name , primary_key ) : condition_template = 't.{}=d.{}' where_clause = ' AND ' . join ( condition_template . format ( pkey , pkey ) for pkey in primary_key ) delete_statement = ( 'DELETE FROM {table} t' ' USING {delete_table} d' ' WHERE {where_clause}' )... | SQL statement for a joined delete from . Generate SQL statement for deleting the intersection of rows between both tables from table referenced by tablename . | 138 | 29 |
1,480 | def copy_from_csv ( conn , file , qualified_name : str , delimiter = ',' , encoding = 'utf8' , null_str = '' , header = True , escape_str = '\\' , quote_char = '"' , force_not_null = None , force_null = None ) : copy_sql = copy_from_csv_sql ( qualified_name , delimiter , encoding , null_str = null_str , header = header... | Copy file - like object to database table . | 164 | 9 |
1,481 | def get_user_tables ( conn ) : query_string = "select schemaname, relname from pg_stat_user_tables;" with conn . cursor ( ) as cursor : cursor . execute ( query_string ) tables = cursor . fetchall ( ) return tables | Retrieve all user tables . | 60 | 6 |
1,482 | def get_column_metadata ( conn , table : str , schema = 'public' ) : query = """\ SELECT attname as name, format_type(atttypid, atttypmod) AS data_type, NOT attnotnull AS nullable FROM pg_catalog.pg_attribute WHERE attrelid=%s::regclass AND attnum > 0 AND NOT attisdropped ORDER BY attnum;""" qualified_name = compile_qu... | Returns column data following db . Column parameter specification . | 130 | 10 |
1,483 | def reflect_table ( conn , table_name , schema = 'public' ) : column_meta = list ( get_column_metadata ( conn , table_name , schema = schema ) ) primary_key_columns = list ( get_primary_keys ( conn , table_name , schema = schema ) ) columns = [ Column ( * * column_data ) for column_data in column_meta ] primary_key = P... | Reflect basic table attributes . | 118 | 6 |
1,484 | def reset ( db_name ) : conn = psycopg2 . connect ( database = 'postgres' ) db = Database ( db_name ) conn . autocommit = True with conn . cursor ( ) as cursor : cursor . execute ( db . drop_statement ( ) ) cursor . execute ( db . create_statement ( ) ) conn . close ( ) | Reset database . | 78 | 4 |
1,485 | def install_extensions ( extensions , * * connection_parameters ) : from postpy . connections import connect conn = connect ( * * connection_parameters ) conn . autocommit = True for extension in extensions : install_extension ( conn , extension ) | Install Postgres extension if available . | 56 | 7 |
1,486 | def update ( self , status ) : logging . info ( 'Executor sends status update {} for task {}' . format ( status . state , status . task_id ) ) return self . driver . sendStatusUpdate ( encode ( status ) ) | Sends a status update to the framework scheduler . | 51 | 11 |
1,487 | def message ( self , data ) : logging . info ( 'Driver sends framework message {}' . format ( data ) ) return self . driver . sendFrameworkMessage ( data ) | Sends a message to the framework scheduler . | 37 | 10 |
1,488 | def get_current_time ( self ) : hms = [ int ( self . get_current_controller_value ( i ) ) for i in range ( 406 , 409 ) ] return datetime . time ( * hms ) | Get current time | 49 | 3 |
1,489 | def get_loco_name ( self ) : ret_str = self . dll . GetLocoName ( ) . decode ( ) if not ret_str : return return ret_str . split ( '.:.' ) | Returns the Provider Product and Engine name . | 48 | 8 |
1,490 | def set_controller_value ( self , index_or_name , value ) : if not isinstance ( index_or_name , int ) : index = self . get_controller_index ( index_or_name ) else : index = index_or_name self . dll . SetControllerValue ( index , ctypes . c_float ( value ) ) | Sets controller value | 78 | 4 |
1,491 | def stop ( self , failover = False ) : logging . info ( 'Stops Scheduler Driver' ) return self . driver . stop ( failover ) | Stops the scheduler driver . | 33 | 7 |
1,492 | def request ( self , requests ) : logging . info ( 'Request resources from Mesos' ) return self . driver . requestResources ( map ( encode , requests ) ) | Requests resources from Mesos . | 35 | 7 |
1,493 | def launch ( self , offer_id , tasks , filters = Filters ( ) ) : logging . info ( 'Launches tasks {}' . format ( tasks ) ) return self . driver . launchTasks ( encode ( offer_id ) , map ( encode , tasks ) , encode ( filters ) ) | Launches the given set of tasks . | 63 | 8 |
1,494 | def kill ( self , task_id ) : logging . info ( 'Kills task {}' . format ( task_id ) ) return self . driver . killTask ( encode ( task_id ) ) | Kills the specified task . | 43 | 6 |
1,495 | def reconcile ( self , statuses ) : logging . info ( 'Reconciles task statuses {}' . format ( statuses ) ) return self . driver . reconcileTasks ( map ( encode , statuses ) ) | Allows the framework to query the status for non - terminal tasks . | 47 | 13 |
1,496 | def accept ( self , offer_ids , operations , filters = Filters ( ) ) : logging . info ( 'Accepts offers {}' . format ( offer_ids ) ) return self . driver . acceptOffers ( map ( encode , offer_ids ) , map ( encode , operations ) , encode ( filters ) ) | Accepts the given offers and performs a sequence of operations on those accepted offers . | 67 | 16 |
1,497 | def acknowledge ( self , status ) : logging . info ( 'Acknowledges status update {}' . format ( status ) ) return self . driver . acknowledgeStatusUpdate ( encode ( status ) ) | Acknowledges the status update . | 39 | 6 |
1,498 | def message ( self , executor_id , slave_id , message ) : logging . info ( 'Sends message `{}` to executor `{}` on slave `{}`' . format ( message , executor_id , slave_id ) ) return self . driver . sendFrameworkMessage ( encode ( executor_id ) , encode ( slave_id ) , message ) | Sends a message from the framework to one of its executors . | 85 | 14 |
1,499 | def _connect_func ( builder , obj , signal_name , handler_name , connect_object , flags , cls ) : if connect_object is None : extra = ( ) else : extra = ( connect_object , ) # The handler name refers to an attribute on the template instance, # so ask GtkBuilder for the template instance template_inst = builder . get_ob... | Handles GtkBuilder signal connect events | 251 | 8 |
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