idx int64 0 63k | question stringlengths 53 5.28k | target stringlengths 5 805 |
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13,100 | def get_info ( self ) : 'Retrieve the data from CrossRef.' escaped_doi = urllib2 . quote ( self . doi , '' ) html = get_resource ( "www.crossref.org" , '/guestquery?queryType=doi&restype=unixref&doi=%s&doi_search=Search' % escaped_doi ) xml_matches = [ ] for m in re . finditer ( '(<doi_records>.*?</doi_records>)' , htm... | Retrieve the data from CrossRef . |
13,101 | def add_backbone_atoms_linearly_from_loop_filepaths ( self , loop_json_filepath , fasta_filepath , residue_ids ) : loop_def = json . loads ( read_file ( loop_json_filepath ) ) assert ( len ( loop_def [ 'LoopSet' ] ) == 1 ) start_res = loop_def [ 'LoopSet' ] [ 0 ] [ 'start' ] end_res = loop_def [ 'LoopSet' ] [ 0 ] [ 'st... | A utility wrapper around add_backbone_atoms_linearly . Adds backbone atoms in a straight line from the first to the last residue of residue_ids . |
13,102 | def add_atoms_linearly ( self , start_atom , end_atom , new_atoms , jitterbug = 0.2 ) : atom_name_map = { 'CA' : ' CA ' , 'C' : ' C ' , 'N' : ' N ' , 'O' : ' O ' , } assert ( start_atom . residue . chain == end_atom . residue . chain ) chain_id = start_atom . residue . chain num_new_atoms = float ( len ( new_atoms )... | A low - level function which adds new_atoms between start_atom and end_atom . This function does not validate the input i . e . the calling functions are responsible for ensuring that the insertion makes sense . |
13,103 | def to_string ( self ) : return '%s %s %s %s %s' % ( self . trait , self . start_position , self . peak_start_position , self . peak_stop_position , self . stop_position ) | Return the string as it should be presented in a MapChart input file . |
13,104 | def main ( ) : preparser = argparse . ArgumentParser ( description = description , add_help = False ) preparser . add_argument ( '--env' , '-e' , dest = 'env' , default = 'development' , help = 'choose application environment' ) namespace , extra = preparser . parse_known_args ( ) env = namespace . env parser = argpars... | The single entry point to glim command line interface . Main method is called from pypi console_scripts key or by glim . py on root . This function initializes a new app given the glim commands and app commands if app exists . |
13,105 | def make_app ( env , commandadapter = None ) : mconfig = import_module ( 'app.config.%s' % env , pass_errors = True ) if mconfig is None and paths . app_exists ( ) : print ( colored ( 'Configuration for "%s" environment is not found' % env , 'red' ) ) return None mstart = import_module ( 'app.start' ) mroutes = import_... | Function creates an app given environment |
13,106 | def callback ( self ) : next = request . args . get ( 'next' ) or None endpoint = 'social.{}.handle' . format ( self . provider ) return url_for ( endpoint , _external = True , next = next ) | Generate callback url for provider |
13,107 | def next ( self ) : next = request . args . get ( 'next' ) if next is None : params = self . default_redirect_params next = url_for ( self . default_redirect_endpoint , ** params ) return next | Where to redirect after authorization |
13,108 | def dispatch_request ( self ) : if current_user . is_authenticated : return redirect ( self . next ) if 'social_data' in session : del session [ 'social_data' ] res = self . app . authorized_response ( ) if res is None : if self . flash : flash ( self . auth_failed_msg , 'danger' ) return redirect ( self . next ) data ... | Handle redirect back from provider |
13,109 | def project ( v , n ) : return v - matmul ( v , n ) * n / ( norm ( n ) ** 2.0 ) | Project Vector v onto plane with normal vector n . |
13,110 | def main ( ) : args = parse_args ( ) if args . version : from . __init__ import __version__ , __release_date__ print ( 'elkme %s (release date %s)' % ( __version__ , __release_date__ ) ) print ( '(c) 2015-2017 46elks AB <hello@46elks.com>' ) print ( small_elk ) exit ( 0 ) conf , conf_status = config . init_config ( arg... | Executed on run |
13,111 | def _build_graph ( self ) -> nx . DiGraph : digraph = nx . DiGraph ( ) for state in self . model . all_states ( ) : self . _number_of_states += 1 for next_state in self . model . available_state ( state ) : self . _number_of_transitions += 1 digraph . add_edge ( self . _transform_state_to_string ( state ) , self . _tra... | Private method to build the graph from the model . |
13,112 | def _transform_state_to_string ( self , state : State ) -> str : return '' . join ( str ( state [ gene ] ) for gene in self . model . genes ) | Private method which transform a state to a string . |
13,113 | def as_dot ( self ) -> str : return nx . drawing . nx_pydot . to_pydot ( self . _graph ) . to_string ( ) | Return as a string the dot version of the graph . |
13,114 | def export_to_dot ( self , filename : str = 'output' ) -> None : with open ( filename + '.dot' , 'w' ) as output : output . write ( self . as_dot ( ) ) | Export the graph to the dot file filename . dot . |
13,115 | def get_duration_measures ( source_file_path , output_path = None , phonemic = False , semantic = False , quiet = False , similarity_file = None , threshold = None ) : args = Args ( ) args . output_path = output_path args . phonemic = phonemic args . semantic = semantic args . source_file_path = source_file_path args .... | Parses input arguments and runs clustering algorithm . |
13,116 | def create_from_textgrid ( self , word_list ) : self . timing_included = True for i , entry in enumerate ( word_list ) : self . unit_list . append ( Unit ( entry , format = "TextGrid" , type = self . type , index_in_timed_response = i ) ) if self . type == "SEMANTIC" : self . lemmatize ( ) self . tokenize ( ) | Fills the ParsedResponse object with a list of TextGrid . Word objects originally from a . TextGrid file . |
13,117 | def lemmatize ( self ) : for unit in self . unit_list : if lemmatizer . lemmatize ( unit . text ) in self . lemmas : unit . text = lemmatizer . lemmatize ( unit . text ) | Lemmatize all Units in self . unit_list . |
13,118 | def tokenize ( self ) : if not self . quiet : print print "Finding compound words..." compound_word_dict = { } for compound_length in range ( 5 , 1 , - 1 ) : compound_word_dict [ compound_length ] = [ name for name in self . names if len ( name . split ( ) ) == compound_length ] current_index = 0 finished = False while... | Tokenizes all multiword names in the list of Units . |
13,119 | def make_compound_word ( self , start_index , how_many ) : if not self . quiet : compound_word = "" for word in self . unit_list [ start_index : start_index + how_many ] : compound_word += " " + word . text print compound_word . strip ( ) , " , "_" . join ( compound_word . split ( ) ) for other_unit in range ( 1 , how_... | Combines two Units in self . unit_list to make a compound word token . |
13,120 | def remove_unit ( self , index ) : if not self . quiet : print "Removing" , self . unit_list [ index ] . text self . unit_list . pop ( index ) | Removes the unit at the given index in self . unit_list . Does not modify any other units . |
13,121 | def combine_same_stem_units ( self , index ) : if not self . quiet : combined_word = "" for word in self . unit_list [ index : index + 2 ] : for original_word in word . original_text : combined_word += " " + original_word print combined_word . strip ( ) , " , "/" . join ( combined_word . split ( ) ) self . unit_list [ ... | Combines adjacent words with the same stem into a single unit . |
13,122 | def display ( self ) : table_list = [ ] table_list . append ( ( "Text" , "Orig. Text" , "Start time" , "End time" , "Phonetic" ) ) for unit in self . unit_list : table_list . append ( ( unit . text , "/" . join ( unit . original_text ) , unit . start_time , unit . end_time , unit . phonetic_representation ) ) print_tab... | Pretty - prints the ParsedResponse to the screen . |
13,123 | def generate_phonetic_representation ( self , word ) : with NamedTemporaryFile ( ) as temp_file : temp_file . write ( word ) t2pargs = [ os . path . abspath ( os . path . join ( os . path . dirname ( __file__ ) , 't2p/t2p' ) ) , '-transcribe' , os . path . join ( data_path , 'cmudict.0.7a.tree' ) , temp_file . name ] t... | Returns a generated phonetic representation for a word . |
13,124 | def modify_phonetic_representation ( self , phonetic_representation ) : for i in range ( len ( phonetic_representation ) ) : phonetic_representation [ i ] = re . sub ( '\d+' , '' , phonetic_representation [ i ] ) multis = [ 'AA' , 'AE' , 'AH' , 'AO' , 'AW' , 'AY' , 'CH' , 'DH' , 'EH' , 'ER' , 'EY' , 'HH' , 'IH' , 'IY' ... | Returns a compact phonetic representation given a CMUdict - formatted representation . |
13,125 | def clean ( self ) : if not self . quiet : print print "Preprocessing input..." print "Raw response:" print self . display ( ) if not self . quiet : print print "Cleaning words..." current_index = 0 while current_index < len ( self . unit_list ) : word = self . unit_list [ current_index ] . text if self . type == "PHON... | Removes any Units that are not applicable given the current semantic or phonetic category . |
13,126 | def load_lsa_information ( self ) : if not ( 49 < int ( self . clustering_parameter ) < 101 ) : raise Exception ( 'Only LSA dimensionalities in the range 50-100' + ' are supported.' ) if not self . quiet : print "Loading LSA term vectors..." with open ( os . path . join ( data_path , self . category + '_' + os . path .... | Loads a dictionary from disk that maps permissible words to their LSA term vectors . |
13,127 | def get_similarity_measures ( self ) : if not self . quiet : print print "Computing" , self . current_similarity_measure , "similarity..." self . compute_similarity_scores ( ) | Helper function for computing similarity measures . |
13,128 | def get_raw_counts ( self ) : words = [ ] labels = [ ] words_said = set ( ) for unit in self . parsed_response : word = unit . text test = False if self . type == "PHONETIC" : test = ( word . startswith ( self . letter ) and "T_" not in word and "E_" not in word and "!" not in word and "FILLEDPAUSE_" not in word and no... | Determines counts for unique words repetitions etc using the raw text response . |
13,129 | def compute_similarity_score ( self , unit1 , unit2 ) : if self . type == "PHONETIC" : word1 = unit1 . phonetic_representation word2 = unit2 . phonetic_representation if self . current_similarity_measure == "phone" : word1_length , word2_length = len ( word1 ) , len ( word2 ) if word1_length > word2_length : word1 , wo... | Returns the similarity score between two words . |
13,130 | def compute_similarity_scores ( self ) : for i , unit in enumerate ( self . parsed_response ) : if i < len ( self . parsed_response ) - 1 : next_unit = self . parsed_response [ i + 1 ] self . similarity_scores . append ( self . compute_similarity_score ( unit , next_unit ) ) if not self . quiet : print self . current_s... | Produce a list of similarity scores for each contiguous pair in a response . |
13,131 | def compute_pairwise_similarity_score ( self ) : pairs = [ ] all_scores = [ ] for i , unit in enumerate ( self . parsed_response ) : for j , other_unit in enumerate ( self . parsed_response ) : if i != j : pair = ( i , j ) rev_pair = ( j , i ) if pair not in pairs and rev_pair not in pairs : score = self . compute_simi... | Computes the average pairwise similarity score between all pairs of Units . |
13,132 | def compute_collection_measures ( self , no_singletons = False ) : prefix = "COLLECTION_" + self . current_similarity_measure + "_" + self . current_collection_type + "_" if no_singletons : prefix += "no_singletons_" if no_singletons : collection_sizes_temp = [ x for x in self . collection_sizes if x != 1 ] else : coll... | Computes summaries of measures using the discovered collections . |
13,133 | def compute_duration_measures ( self ) : prefix = "TIMING_" + self . current_similarity_measure + "_" + self . current_collection_type + "_" if self . response_format == 'TextGrid' : self . compute_response_vowel_duration ( "TIMING_" ) self . compute_response_continuant_duration ( "TIMING_" ) self . compute_between_col... | Helper function for computing measures derived from timing information . |
13,134 | def compute_response_vowel_duration ( self , prefix ) : durations = [ ] for word in self . full_timed_response : if word . phones : for phone in word . phones : if phone . string in self . vowels : durations . append ( phone . end - phone . start ) self . measures [ prefix + 'response_vowel_duration_mean' ] = get_mean ... | Computes mean vowel duration in entire response . |
13,135 | def compute_between_collection_interval_duration ( self , prefix ) : durations = [ ] for collection in self . collection_list : start = collection [ 0 ] . start_time end = collection [ - 1 ] . end_time durations . append ( ( start , end ) ) interstices = [ durations [ i + 1 ] [ 0 ] - durations [ i ] [ 1 ] for i , d in ... | Calculates BETWEEN - collection intervals for the current collection and measure type and takes their mean . |
13,136 | def compute_within_collection_interval_duration ( self , prefix ) : interstices = [ ] for cluster in self . collection_list : if len ( cluster ) > 1 : for i in range ( len ( cluster ) ) : if i != len ( cluster ) - 1 : interstice = cluster [ i + 1 ] . start_time - cluster [ i ] . end_time interstices . append ( intersti... | Calculates mean between - word duration WITHIN collections . |
13,137 | def compute_within_collection_vowel_duration ( self , prefix , no_singletons = False ) : if no_singletons : min_size = 2 else : prefix += "no_singletons_" min_size = 1 durations = [ ] for cluster in self . collection_list : if len ( cluster ) >= min_size : for word in cluster : word = self . full_timed_response [ word ... | Computes the mean duration of vowels from Units within clusters . |
13,138 | def print_output ( self ) : if self . response_format == "csv" : for key in self . measures : if "TIMING_" in key : self . measures [ key ] = "NA" if not self . quiet : print print self . type . upper ( ) + " RESULTS:" keys = [ e for e in self . measures if 'COUNT_' in e ] keys . sort ( ) print "Counts:" print_table ( ... | Outputs final list of measures to screen a csv file . |
13,139 | def insert_child ( self , child_pid , index = - 1 ) : if child_pid . status != PIDStatus . REGISTERED : raise PIDRelationConsistencyError ( "Version PIDs should have status 'REGISTERED'. Use " "insert_draft_child to insert 'RESERVED' draft PID." ) with db . session . begin_nested ( ) : draft = self . draft_child if dra... | Insert a Version child PID . |
13,140 | def remove_child ( self , child_pid ) : if child_pid . status == PIDStatus . RESERVED : raise PIDRelationConsistencyError ( "Version PIDs should not have status 'RESERVED'. Use " "remove_draft_child to remove a draft PID." ) with db . session . begin_nested ( ) : super ( PIDNodeVersioning , self ) . remove_child ( chil... | Remove a Version child PID . |
13,141 | def insert_draft_child ( self , child_pid ) : if child_pid . status != PIDStatus . RESERVED : raise PIDRelationConsistencyError ( "Draft child should have status 'RESERVED'" ) if not self . draft_child : with db . session . begin_nested ( ) : super ( PIDNodeVersioning , self ) . insert_child ( child_pid , index = - 1 )... | Insert a draft child to versioning . |
13,142 | def remove_draft_child ( self ) : if self . draft_child : with db . session . begin_nested ( ) : super ( PIDNodeVersioning , self ) . remove_child ( self . draft_child , reorder = True ) | Remove the draft child from versioning . |
13,143 | def update_redirect ( self ) : if self . last_child : self . _resolved_pid . redirect ( self . last_child ) elif any ( map ( lambda pid : pid . status not in [ PIDStatus . DELETED , PIDStatus . REGISTERED , PIDStatus . RESERVED ] , super ( PIDNodeVersioning , self ) . children . all ( ) ) ) : raise PIDRelationConsisten... | Update the parent redirect to the current last child . |
13,144 | def feedback ( request ) : if request . method == 'GET' : return render ( request , 'feedback_feedback.html' , { } , help_text = feedback . __doc__ ) if request . method == 'POST' : feedback_data = json_body ( request . body . decode ( "utf-8" ) ) feedback_data [ 'user_agent' ] = Session . objects . get_current_session... | Send feedback to the authors of the system . |
13,145 | def rating ( request ) : if request . method == 'GET' : return render ( request , 'feedback_rating.html' , { } , help_text = rating . __doc__ ) if request . method == 'POST' : data = json_body ( request . body . decode ( "utf-8" ) ) if data [ 'value' ] not in list ( range ( 1 , 9 ) ) : return render_json ( request , { ... | Rate the current practice . |
13,146 | def colour ( colour , message , bold = False ) : return style ( fg = colour , text = message , bold = bold ) | Color a message |
13,147 | def customFilter ( self , filterFunc ) : ret = self . __class__ ( ) for item in self : if filterFunc ( item ) : ret . append ( item ) return ret | customFilter - Apply a custom filter to elements and return a QueryableList of matches |
13,148 | def sort_by ( self , fieldName , reverse = False ) : return self . __class__ ( sorted ( self , key = lambda item : self . _get_item_value ( item , fieldName ) , reverse = reverse ) ) | sort_by - Return a copy of this collection sorted by the given fieldName . |
13,149 | def uri ( self ) : return self . uri_template . format ( host = self . host , port = "" if self . port is None else self . port , database = self . database , username = self . username , password = "" if self . password is None else self . password , has_password = "" if self . password is None else ":" , has_port = "... | Return sqlalchemy connect string URI . |
13,150 | def from_json ( cls , json_file , json_path = None , key_mapping = None ) : cls . _validate_key_mapping ( key_mapping ) with open ( json_file , "rb" ) as f : data = json . loads ( f . read ( ) . decode ( "utf-8" ) ) return cls . _from_json_data ( data , json_path , key_mapping ) | Load connection credential from json file . |
13,151 | def from_s3_json ( cls , bucket_name , key , json_path = None , key_mapping = None , aws_profile = None , aws_access_key_id = None , aws_secret_access_key = None , region_name = None ) : import boto3 ses = boto3 . Session ( aws_access_key_id = aws_access_key_id , aws_secret_access_key = aws_secret_access_key , region_n... | Load database credential from json on s3 . |
13,152 | def from_env ( cls , prefix , kms_decrypt = False , aws_profile = None ) : if len ( prefix ) < 1 : raise ValueError ( "prefix can't be empty" ) if len ( set ( prefix ) . difference ( set ( string . ascii_uppercase + "_" ) ) ) : raise ValueError ( "prefix can only use [A-Z] and '_'!" ) if not prefix . endswith ( "_" ) :... | Load database credential from env variable . |
13,153 | def to_dict ( self ) : return dict ( host = self . host , port = self . port , database = self . database , username = self . username , password = self . password , ) | Convert credentials into a dict . |
13,154 | def start_debugging ( ) : exc_type , exc_value , exc_tb = sys . exc_info ( ) if hasattr ( exc_value , '_ipdbugger_let_raise' ) : raise_ ( * sys . exc_info ( ) ) print ( ) for line in traceback . format_exception ( exc_type , exc_value , exc_tb ) : print ( colored ( line , 'red' ) , end = ' ' ) test_frame = sys . _getfr... | Start a debugging session after catching an exception . |
13,155 | def get_last_lineno ( node ) : max_lineno = 0 if hasattr ( node , "lineno" ) : max_lineno = node . lineno for _ , field in ast . iter_fields ( node ) : if isinstance ( field , list ) : for value in field : if isinstance ( value , ast . AST ) : max_lineno = max ( max_lineno , get_last_lineno ( value ) ) elif isinstance ... | Recursively find the last line number of the ast node . |
13,156 | def do_raise ( self , arg ) : self . do_continue ( arg ) _ , exc_value , _ = self . exc_info exc_value . _ipdbugger_let_raise = True raise_ ( * self . exc_info ) | Raise the last exception caught . |
13,157 | def do_retry ( self , arg ) : prev_line = self . curframe . f_lineno - 1 while True : try : self . curframe . f_lineno = prev_line break except ValueError : prev_line -= 1 self . do_jump ( prev_line ) self . do_continue ( arg ) return 1 | Rerun the previous command . |
13,158 | def dispatch_line ( self , frame ) : callback = TerminalPdb . dispatch_line ( self , frame ) if self . stoplineno == - 1 : return None return callback | Handle line action and return the next line callback . |
13,159 | def wrap_with_try ( self , node ) : handlers = [ ] if self . ignore_exceptions is None : handlers . append ( ast . ExceptHandler ( type = None , name = None , body = [ ast . Raise ( ) ] ) ) else : ignores_nodes = self . ignore_exceptions handlers . append ( ast . ExceptHandler ( type = ast . Tuple ( ignores_nodes , ast... | Wrap an ast node in a try node to enter debug on exception . |
13,160 | def try_except_handler ( self , node ) : excepted_types = [ ] for handler in node . handlers : if handler . type is None : excepted_types = None break if isinstance ( handler . type , ast . Tuple ) : excepted_types . extend ( [ exception_type for exception_type in handler . type . elts ] ) else : excepted_types . appen... | Handler for try except statement to ignore excepted exceptions . |
13,161 | def visit_Call ( self , node ) : if self . depth == 0 : return node if self . ignore_exceptions is None : ignore_exceptions = ast . Name ( "None" , ast . Load ( ) ) else : ignore_exceptions = ast . List ( self . ignore_exceptions , ast . Load ( ) ) catch_exception_type = self . catch_exception if self . catch_exception... | Propagate debug wrapper into inner function calls if needed . |
13,162 | def get_qtls_from_rqtl_data ( matrix , lod_threshold ) : t_matrix = list ( zip ( * matrix ) ) qtls = [ [ 'Trait' , 'Linkage Group' , 'Position' , 'Exact marker' , 'LOD' ] ] for row in t_matrix [ 3 : ] : lgroup = None max_lod = None peak = None cnt = 1 while cnt < len ( row ) : if lgroup is None : lgroup = t_matrix [ 1 ... | Retrieve the list of significants QTLs for the given input matrix and using the specified LOD threshold . This assumes one QTL per linkage group . |
13,163 | def save_session ( self , * args , ** kwargs ) : if g . get ( 'stateless_sessions' ) : return return super ( BoilerSessionInterface , self ) . save_session ( * args , ** kwargs ) | Save session Skip setting session cookie if requested via g . stateless_sessions |
13,164 | def prune_old ( self ) : path = self . pubdir dirmask = self . dirmask expire = self . expire expire_limit = int ( time . time ( ) ) - ( 86400 * expire ) logger . info ( 'Pruning directories older than %d days' , expire ) if not os . path . isdir ( path ) : logger . warning ( 'Dir %r not found -- skipping pruning' , pa... | Removes the directories that are older than a certain date . |
13,165 | def send_report ( self , report_parts ) : logger . info ( 'Checking and creating the report directory' ) report_parts = sorted ( filter ( lambda x : x . fmt in self . formats , report_parts ) , key = lambda x : self . formats . index ( x . fmt ) ) workdir = os . path . join ( self . pubdir , self . dirname ) if not os ... | Publish the report parts to local files . Each report part is a text with a title and specific extension . For html and plaintext sending the report part is unique for csv send also the stats and unparsed string are plain text and report items are csv texts . |
13,166 | def parse ( self ) : self . _parse ( self . method ) return list ( set ( [ deco for deco in self . decos if deco ] ) ) | Return the list of string of all the decorators found |
13,167 | def filter_304_headers ( headers ) : return [ ( k , v ) for k , v in headers if k . lower ( ) not in _filter_from_304 ] | Filter a list of headers to include in a 304 Not Modified response . |
13,168 | def response ( code , body = '' , etag = None , last_modified = None , expires = None , ** kw ) : if etag is not None : if not ( etag [ 0 ] == '"' and etag [ - 1 ] == '"' ) : etag = '"%s"' % etag kw [ 'etag' ] = etag if last_modified is not None : kw [ 'last_modified' ] = datetime_to_httpdate ( last_modified ) if expir... | Helper to build an HTTP response . |
13,169 | def body ( self ) : if self . _body is None : raw_body = self . _raw_body if self . _body_writer is None : self . _body = raw_body ( ) if callable ( raw_body ) else raw_body else : self . _body = self . _body_writer ( raw_body ) return self . _body | Seralizes and returns the response body . |
13,170 | def set_cookie ( self , key , value = '' , max_age = None , path = '/' , domain = None , secure = False , httponly = False , expires = None ) : key , value = key . encode ( 'utf-8' ) , value . encode ( 'utf-8' ) cookie = SimpleCookie ( { key : value } ) m = cookie [ key ] if max_age is not None : if isinstance ( max_ag... | Set a response cookie . |
13,171 | def conditional_to ( self , request ) : if not self . code == 200 : return self request_headers = request . headers response_headers = self . headers if_none_match = request_headers . get ( 'If-None-Match' ) if_modified_since = request_headers . get ( 'If-Modified-Since' ) etag_ok , date_ok = False , False if if_none_m... | Return a response that is conditional to a given request . |
13,172 | def _get_ukko_report ( ) : with urllib . request . urlopen ( URL_UKKO_REPORT ) as response : ret = str ( response . read ( ) ) return ret | Get Ukko s report from the fixed URL . |
13,173 | def get_nodes ( n = 8 , exclude = [ ] , loop = None ) : report = _get_ukko_report ( ) nodes = _parse_ukko_report ( report ) ret = [ ] while len ( ret ) < n and len ( nodes ) > 0 : node = nodes [ 0 ] if node not in exclude : reachable = True if loop is not None : reachable = loop . run_until_complete ( _test_node ( node... | Get Ukko nodes with the least amount of load . |
13,174 | def get_unix_ioctl_terminal_size ( ) : def ioctl_gwinsz ( fd ) : try : import fcntl import termios import struct return struct . unpack ( 'hh' , fcntl . ioctl ( fd , termios . TIOCGWINSZ , '1234' ) ) except ( IOError , OSError ) : return None cr = ioctl_gwinsz ( 0 ) or ioctl_gwinsz ( 1 ) or ioctl_gwinsz ( 2 ) if not cr... | Get the terminal size of a UNIX terminal using the ioctl UNIX command . |
13,175 | def add_marker_to_qtl ( qtl , map_list ) : closest = '' diff = None for marker in map_list : if qtl [ 1 ] == marker [ 1 ] : tmp_diff = float ( qtl [ 2 ] ) - float ( marker [ 2 ] ) if diff is None or abs ( diff ) > abs ( tmp_diff ) : diff = tmp_diff closest = marker if closest != '' : closest = closest [ 0 ] return clos... | Add the closest marker to the given QTL . |
13,176 | def add_marker_to_qtls ( qtlfile , mapfile , outputfile = 'qtls_with_mk.csv' ) : qtl_list = read_input_file ( qtlfile , ',' ) map_list = read_input_file ( mapfile , ',' ) if not qtl_list or not map_list : return qtl_list [ 0 ] . append ( 'Closest marker' ) qtls = [ ] qtls . append ( qtl_list [ 0 ] ) for qtl in qtl_list... | This function adds to a list of QTLs the closest marker to the QTL peak . |
13,177 | def addFilter ( self , filterMethod = FILTER_METHOD_AND , ** kwargs ) : filterMethod = filterMethod . upper ( ) if filterMethod not in FILTER_METHODS : raise ValueError ( 'Unknown filter method, %s. Must be one of: %s' % ( str ( filterMethod ) , repr ( FILTER_METHODS ) ) ) self . filters . append ( ( filterMethod , kwa... | addFilter - Add a filter to this query . |
13,178 | def execute ( self , lst ) : from . import QueryableListMixed if not issubclass ( lst . __class__ , QueryableListBase ) : lst = QueryableListMixed ( lst ) filters = copy . copy ( self . filters ) nextFilter = filters . popleft ( ) while nextFilter : ( filterMethod , filterArgs ) = nextFilter lst = self . _applyFilter (... | execute - Execute the series of filters in order on the provided list . |
13,179 | def copy ( self ) : ret = QueryBuilder ( ) ret . filters = copy . copy ( self . filters ) return ret | copy - Create a copy of this query . |
13,180 | def _applyFilter ( lst , filterMethod , filterArgs ) : if filterMethod == FILTER_METHOD_AND : return lst . filterAnd ( ** filterArgs ) else : return lst . filterOr ( ** filterArgs ) | _applyFilter - Applies the given filter method on a set of args |
13,181 | def _raise_corsair_error ( self , error = None , message = "" ) : if error is None : error = self . last_error ( ) raise error ( message ) | Raise error message based on the last reported error from the SDK |
13,182 | def device_count ( self ) : device_count = get_device_count ( self . corsair_sdk ) if device_count == - 1 : self . _raise_corsair_error ( ) return device_count | Find amount of CUE devices |
13,183 | def led_id_from_char ( self , char ) : led_id = get_led_id_for_key_name ( self . corsair_sdk , bytes ( char ) ) if led_id == 0 : self . _raise_corsair_error ( ) return led_id | Get id of a led by the letter Only between A - Z |
13,184 | def set_led ( self , led_id , color ) : if not set_leds_color ( self . corsair_sdk , LedColor ( led_id , * color ) ) : self . _raise_corsair_error ( ) return True | Set color of an led |
13,185 | def request_control ( self , device_id , access_mode = True ) : if access_mode : if not request_control ( self . corsair_sdk , device_id ) : self . _raise_corsair_error ( ) return True else : self . reload ( ) | Request exclusive control of device |
13,186 | def device ( self , device_id , * args , ** kwargs ) : return Device ( device_id , self . corsair_sdk , self . _corsair_sdk_path , * args , ** kwargs ) | Return a Device object based on id |
13,187 | def device_info ( self , device_id = None ) : if device_id is None : device_id = self . device_id return get_device_info ( self . corsair_sdk , device_id ) | Return device information if device_id is not specified return for this device |
13,188 | def get_obsolete_acc_to_uniparc ( acc ) : contents = http_get ( 'www.uniprot.org/uniparc/?query={0}' . format ( acc ) ) mtchs = re . findall ( r'"UPI[A-Z0-9]+?"' , contents , re . DOTALL ) uniparc_id = set ( [ m [ 1 : - 1 ] for m in mtchs ] ) if len ( uniparc_id ) == 1 : return uniparc_id . pop ( ) elif len ( uniparc_i... | Tries to determine the UniParc ID for obsolete ACCs which are not returned using uniprot_map . |
13,189 | def get_common_PDB_IDs ( pdb_id , cache_dir = None , exception_on_failure = True ) : m = pdb_to_uniparc ( [ pdb_id ] , cache_dir = cache_dir ) UniProtACs = [ ] if pdb_id in m : for entry in m [ pdb_id ] : if entry . UniProtACs : UniProtACs . extend ( entry . UniProtACs ) elif exception_on_failure : raise Exception ( 'N... | This function takes a PDB ID maps it to UniProt ACCs then returns the common set of PDB IDs related to those ACCs . The purpose is to find any PDB files related to pdb_id particularly for complexes such that the other PDB files contain identical sequences or mutant complexes . |
13,190 | def _parse_sequence_tag ( self ) : entry_tag = self . entry_tag sequence_tags = [ child for child in entry_tag . childNodes if child . nodeType == child . ELEMENT_NODE and child . tagName == 'sequence' ] assert ( len ( sequence_tags ) == 1 ) sequence_tag = sequence_tags [ 0 ] self . atomic_mass = float ( sequence_tag .... | Parses the sequence and atomic mass . |
13,191 | def cool_paginate ( context , ** kwargs ) -> dict : names = ( 'size' , 'next_name' , 'previous_name' , 'elastic' , 'page_obj' , ) return_dict = { name : value for name , value in zip ( names , map ( kwargs . get , names ) ) } if context . get ( 'request' ) : return_dict [ 'request' ] = context [ 'request' ] else : rais... | Main function for pagination process . |
13,192 | def time_restarts ( data_path ) : path = os . path . join ( data_path , 'last_restarted' ) if not os . path . isfile ( path ) : with open ( path , 'a' ) : os . utime ( path , None ) last_modified = os . stat ( path ) . st_mtime with open ( path , 'a' ) : os . utime ( path , None ) now = os . stat ( path ) . st_mtime di... | When called will create a file and measure its mtime on restarts |
13,193 | def from_stmt ( stmt , engine , ** kwargs ) : result_proxy = engine . execute ( stmt , ** kwargs ) return from_db_cursor ( result_proxy . cursor ) | Execute a query in form of texture clause return the result in form of |
13,194 | def compute_stability_classification ( self , predicted_data , record , dataframe_record ) : stability_classification , stability_classication_x_cutoff , stability_classication_y_cutoff = None , self . stability_classication_x_cutoff , self . stability_classication_y_cutoff if record [ 'DDG' ] != None : stability_class... | Calculate the stability classification for this case . |
13,195 | def compute_absolute_error ( self , predicted_data , record , dataframe_record ) : absolute_error = abs ( record [ 'DDG' ] - predicted_data [ self . ddg_analysis_type ] ) dataframe_record [ 'AbsoluteError' ] = absolute_error | Calculate the absolute error for this case . |
13,196 | def count_residues ( self , record , pdb_record ) : mutations = self . get_record_mutations ( record ) pdb_chains = set ( [ m [ 'Chain' ] for m in mutations ] ) assert ( len ( pdb_chains ) == 1 ) pdb_chain = pdb_chains . pop ( ) return len ( pdb_record . get ( 'Chains' , { } ) . get ( pdb_chain , { } ) . get ( 'Sequenc... | Count the number of residues in the chains for the case . |
13,197 | def full_analysis ( self , analysis_set , output_directory , verbose = True , compile_pdf = True , quick_plots = False ) : if not os . path . isdir ( output_directory ) : os . makedirs ( output_directory ) self . analysis_directory = output_directory self . calculate_metrics ( analysis_set = analysis_set , analysis_dir... | Combines calculate_metrics write_dataframe_to_csv and plot |
13,198 | def get_unique_ajps ( benchmark_runs ) : br_ajps = { } for br in benchmark_runs : for ajp in br . additional_join_parameters : if ajp not in br_ajps : br_ajps [ ajp ] = set ( ) br_ajps [ ajp ] . add ( br . additional_join_parameters [ ajp ] [ 'short_name' ] ) unique_ajps = [ ] for ajp in br_ajps : if len ( br_ajps [ aj... | Determines which join parameters are unique |
13,199 | def plot_optimum_prediction_fraction_correct_cutoffs_over_range ( self , analysis_set , min_stability_classication_x_cutoff , max_stability_classication_x_cutoff , suppress_plot = False , analysis_file_prefix = None , verbose = True ) : analysis_set_prefix = '' plot_filename = None if not suppress_plot : output_filenam... | Plots the optimum cutoff for the predictions to maximize the fraction correct metric over a range of experimental cutoffs . Returns the average scalar corresponding to the best value of fraction correct over a range of cutoff values for the experimental cutoffs . |
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