idx int64 0 63k | question stringlengths 61 4.03k | target stringlengths 6 1.23k |
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11,500 | def get_rotation_parameters ( phases , magnitudes ) : z_thetas = [ ] y_thetas = [ ] new_phases = [ ] new_magnitudes = [ ] for i in range ( 0 , len ( phases ) , 2 ) : phi = phases [ i ] psi = phases [ i + 1 ] z_thetas . append ( phi - psi ) kappa = ( phi + psi ) / 2. new_phases . append ( kappa ) a = magnitudes [ i ] b ... | Simulates one step of rotations . |
11,501 | def get_reversed_unification_program ( angles , control_indices , target , controls , mode ) : if mode == 'phase' : gate = RZ elif mode == 'magnitude' : gate = RY else : raise ValueError ( "mode must be \'phase\' or \'magnitude\'" ) reversed_gates = [ ] for j in range ( len ( angles ) ) : if angles [ j ] != 0 : reverse... | Gets the Program representing the reversed circuit for the decomposition of the uniformly controlled rotations in a unification step . |
11,502 | def get_ancestors ( self ) : node = self ancestor_list = [ ] while node . parent is not None : ancestor_list . append ( node . parent ) node = node . parent return ancestor_list | Returns a list of ancestors of the node . Ordered from the earliest . |
11,503 | def bitwise_dot_product ( bs0 : str , bs1 : str ) -> str : if len ( bs0 ) != len ( bs1 ) : raise ValueError ( "Bit strings are not of equal length" ) return str ( sum ( [ int ( bs0 [ i ] ) * int ( bs1 [ i ] ) for i in range ( len ( bs0 ) ) ] ) % 2 ) | A helper to calculate the bitwise dot - product between two string representing bit - vectors |
11,504 | def notebook_mode ( m ) : global NOTEBOOK_MODE global TRANGE NOTEBOOK_MODE = m if NOTEBOOK_MODE : TRANGE = tqdm . tnrange else : TRANGE = tqdm . trange | Configure whether this module should assume that it is being run from a jupyter notebook . This sets some global variables related to how progress for long measurement sequences is indicated . |
11,505 | def sample_outcomes ( probs , n ) : dist = np . cumsum ( probs ) rs = np . random . rand ( n ) return np . array ( [ ( np . where ( r < dist ) [ 0 ] [ 0 ] ) for r in rs ] ) | For a discrete probability distribution probs with outcomes 0 1 ... k - 1 draw n random samples . |
11,506 | def sample_bad_readout ( program , num_samples , assignment_probs , cxn ) : wf = cxn . wavefunction ( program ) return sample_outcomes ( assignment_probs . dot ( abs ( wf . amplitudes . ravel ( ) ) ** 2 ) , num_samples ) | Generate n samples of measuring all outcomes of a Quil program assuming the assignment probabilities assignment_probs by simulating the wave function on a qvm QVMConnection cxn |
11,507 | def plot_pauli_transfer_matrix ( ptransfermatrix , ax , labels , title ) : im = ax . imshow ( ptransfermatrix , interpolation = "nearest" , cmap = rigetti_3_color_cm , vmin = - 1 , vmax = 1 ) dim = len ( labels ) plt . colorbar ( im , ax = ax ) ax . set_xticks ( range ( dim ) ) ax . set_xlabel ( "Input Pauli Operator" ... | Visualize the Pauli Transfer Matrix of a process . |
11,508 | def state_histogram ( rho , ax = None , title = "" , threshold = 0.001 ) : rho_amps = rho . data . toarray ( ) . ravel ( ) nqc = int ( round ( np . log2 ( rho . shape [ 0 ] ) ) ) if ax is None : fig = plt . figure ( figsize = ( 10 , 6 ) ) ax = Axes3D ( fig , azim = - 35 , elev = 35 ) cmap = rigetti_4_color_cm norm = mp... | Visualize a density matrix as a 3d bar plot with complex phase encoded as the bar color . |
11,509 | def bitlist_to_int ( bitlist ) : ret = 0 for b in bitlist : ret = ( ret << 1 ) | ( int ( b ) & 1 ) return ret | Convert a binary bitstring into the corresponding unsigned integer . |
11,510 | def sample_assignment_probs ( qubits , nsamples , cxn ) : num_qubits = len ( qubits ) dimension = 2 ** num_qubits hists = [ ] preps = basis_state_preps ( * qubits ) jobs = [ ] _log . info ( 'Submitting jobs...' ) for jj , p in izip ( TRANGE ( dimension ) , preps ) : jobs . append ( cxn . run_and_measure_async ( p , qub... | Sample the assignment probabilities of qubits using nsamples per measurement and then compute the estimated assignment probability matrix . See the docstring for estimate_assignment_probs for more information . |
11,511 | def run_in_parallel ( programs , nsamples , cxn , shuffle = True ) : if shuffle : n_groups = len ( programs ) n_progs_per_group = len ( programs [ 0 ] ) permutations = np . outer ( np . ones ( n_groups , dtype = int ) , np . arange ( n_progs_per_group , dtype = int ) ) inverse_permutations = np . zeros_like ( permutati... | Take sequences of Protoquil programs on disjoint qubits and execute a single sequence of programs that executes the input programs in parallel . Optionally randomize within each qubit - specific sequence . |
11,512 | def remove_imaginary_terms ( pauli_sums : PauliSum ) -> PauliSum : if not isinstance ( pauli_sums , PauliSum ) : raise TypeError ( "not a pauli sum. please give me one" ) new_term = sI ( 0 ) * 0.0 for term in pauli_sums : new_term += term_with_coeff ( term , term . coefficient . real ) return new_term | Remove the imaginary component of each term in a Pauli sum . |
11,513 | def get_rotation_program ( pauli_term : PauliTerm ) -> Program : meas_basis_change = Program ( ) for index , gate in pauli_term : if gate == 'X' : meas_basis_change . inst ( RY ( - np . pi / 2 , index ) ) elif gate == 'Y' : meas_basis_change . inst ( RX ( np . pi / 2 , index ) ) elif gate == 'Z' : pass else : raise Val... | Generate a rotation program so that the pauli term is diagonal . |
11,514 | def controlled ( m : np . ndarray ) -> np . ndarray : rows , cols = m . shape assert rows == cols n = rows I = np . eye ( n ) Z = np . zeros ( ( n , n ) ) controlled_m = np . bmat ( [ [ I , Z ] , [ Z , m ] ] ) return controlled_m | Make a one - qubit - controlled version of a matrix . |
11,515 | def phase_estimation ( U : np . ndarray , accuracy : int , reg_offset : int = 0 ) -> Program : assert isinstance ( accuracy , int ) rows , cols = U . shape m = int ( log2 ( rows ) ) output_qubits = range ( 0 , accuracy ) U_qubits = range ( accuracy , accuracy + m ) p = Program ( ) ro = p . declare ( 'ro' , 'BIT' , len ... | Generate a circuit for quantum phase estimation . |
11,516 | def binary_float_to_decimal_float ( number : Union [ float , str ] ) -> float : if isinstance ( number , str ) : if number [ 0 ] == '-' : n_sign = - 1 else : n_sign = 1 elif isinstance ( number , float ) : n_sign = np . sign ( number ) number = str ( number ) deci = 0 for ndx , val in enumerate ( number . split ( '.' )... | Convert binary floating point to decimal floating point . |
11,517 | def measurements_to_bf ( measurements : np . ndarray ) -> float : try : measurements . sum ( axis = 0 ) except AttributeError : measurements = np . asarray ( measurements ) finally : stats = measurements . sum ( axis = 0 ) / len ( measurements ) stats_str = [ str ( int ( i ) ) for i in np . round ( stats [ : : - 1 ] [ ... | Convert measurements into gradient binary fraction . |
11,518 | def amplification_circuit ( algorithm : Program , oracle : Program , qubits : List [ int ] , num_iter : int , decompose_diffusion : bool = False ) -> Program : program = Program ( ) uniform_superimposer = Program ( ) . inst ( [ H ( qubit ) for qubit in qubits ] ) program += uniform_superimposer if decompose_diffusion :... | Returns a program that does num_iter rounds of amplification given a measurement - less algorithm an oracle and a list of qubits to operate on . |
11,519 | def _operator_generator ( index , conj ) : pterm = PauliTerm ( 'I' , 0 , 1.0 ) Zstring = PauliTerm ( 'I' , 0 , 1.0 ) for j in range ( index ) : Zstring = Zstring * PauliTerm ( 'Z' , j , 1.0 ) pterm1 = Zstring * PauliTerm ( 'X' , index , 0.5 ) scalar = 0.5 * conj * 1.0j pterm2 = Zstring * PauliTerm ( 'Y' , index , scala... | Internal method to generate the appropriate operator |
11,520 | def maxcut_qaoa ( graph , steps = 1 , rand_seed = None , connection = None , samples = None , initial_beta = None , initial_gamma = None , minimizer_kwargs = None , vqe_option = None ) : if not isinstance ( graph , nx . Graph ) and isinstance ( graph , list ) : maxcut_graph = nx . Graph ( ) for edge in graph : maxcut_g... | Max cut set up method |
11,521 | def default_rotations ( * qubits ) : for gates in cartesian_product ( TOMOGRAPHY_GATES . keys ( ) , repeat = len ( qubits ) ) : tomography_program = Program ( ) for qubit , gate in izip ( qubits , gates ) : tomography_program . inst ( gate ( qubit ) ) yield tomography_program | Generates the Quil programs for the tomographic pre - and post - rotations of any number of qubits . |
11,522 | def default_channel_ops ( nqubits ) : for gates in cartesian_product ( TOMOGRAPHY_GATES . values ( ) , repeat = nqubits ) : yield qt . tensor ( * gates ) | Generate the tomographic pre - and post - rotations of any number of qubits as qutip operators . |
11,523 | def is_functional ( cls ) : if not cls . _tested : cls . _tested = True np . random . seed ( SEED ) test_problem_dimension = 10 mat = np . random . randn ( test_problem_dimension , test_problem_dimension ) posmat = mat . dot ( mat . T ) posvar = cvxpy . Variable ( test_problem_dimension , test_problem_dimension ) prob ... | Checks lazily whether a convex solver is installed that handles positivity constraints . |
11,524 | def measure_wf_coefficients ( prep_program , coeff_list , reference_state , quantum_resource , variance_bound = 1.0E-6 ) : num_qubits = len ( prep_program . get_qubits ( ) ) normalizer_ops = projector_generator ( reference_state , reference_state ) c0_coeff , _ , _ = estimate_locally_commuting_operator ( prep_program ,... | Measure a set of coefficients with a phase relative to the reference_state |
11,525 | def measure_pure_state ( prep_program , reference_state , quantum_resource , variance_bound = 1.0E-6 ) : num_qubits = len ( prep_program . get_qubits ( ) ) amplitudes_to_measure = list ( range ( 2 ** num_qubits ) ) amplitudes = measure_wf_coefficients ( prep_program , amplitudes_to_measure , reference_state , quantum_r... | Measure the coefficients of the pure state |
11,526 | def build ( self ) : self . defined_gates = set ( STANDARD_GATE_NAMES ) prog = self . _recursive_builder ( self . operation , self . gate_name , self . control_qubits , self . target_qubit ) return prog | Builds this controlled gate . |
11,527 | def _defgate ( self , program , gate_name , gate_matrix ) : new_program = pq . Program ( ) new_program += program if gate_name not in self . defined_gates : new_program . defgate ( gate_name , gate_matrix ) self . defined_gates . add ( gate_name ) return new_program | Defines a gate named gate_name with matrix gate_matrix in program . In addition updates self . defined_gates to track what has been defined . |
11,528 | def parity_even_p ( state , marked_qubits ) : assert isinstance ( state , int ) , f"{state} is not an integer. Must call parity_even_p with an integer state." mask = 0 for q in marked_qubits : mask |= 1 << q return bin ( mask & state ) . count ( "1" ) % 2 == 0 | Calculates the parity of elements at indexes in marked_qubits |
11,529 | def vqe_run ( self , variational_state_evolve , hamiltonian , initial_params , gate_noise = None , measurement_noise = None , jacobian = None , qc = None , disp = None , samples = None , return_all = False ) : self . _disp_fun = disp if disp is not None else lambda x : None iteration_params = [ ] expectation_vals = [ ]... | functional minimization loop . |
11,530 | def _get_path_from_parent ( self , parent ) : if hasattr ( self , 'get_path_from_parent' ) : return self . get_path_from_parent ( parent ) if self . model is parent : return [ ] model = self . concrete_model chain = model . _meta . get_base_chain ( parent ) or [ ] chain . reverse ( ) chain . append ( model ) path = [ ]... | Return a list of PathInfos containing the path from the parent model to the current model or an empty list if parent is not a parent of the current model . |
11,531 | def patience_sort ( xs ) : pile_tops = list ( ) for x in xs : pile = bisect . bisect_left ( pile_tops , x ) if pile == len ( pile_tops ) : pile_tops . append ( x ) else : pile_tops [ pile ] = x yield x , pile | Patience sort an iterable xs . |
11,532 | def longest_monotonic_subseq_length ( xs ) : li = longest_increasing_subseq_length ( xs ) ld = longest_decreasing_subseq_length ( xs ) return max ( li , ld ) , li - ld | Return the length of the longest monotonic subsequence of xs second return value is the difference between increasing and decreasing lengths . |
11,533 | def longest_increasing_subsequence ( xs ) : piles = [ [ ] ] for x , p in patience_sort ( xs ) : if p + 1 == len ( piles ) : piles . append ( [ ] ) piles [ p + 1 ] . append ( ( x , len ( piles [ p ] ) - 1 ) ) npiles = len ( piles ) - 1 prev = 0 lis = list ( ) for pile in range ( npiles , 0 , - 1 ) : x , prev = piles [ p... | Return a longest increasing subsequence of xs . |
11,534 | def backtracking ( a , L , bestsofar ) : w , j = max ( L . items ( ) ) while j != - 1 : yield j w , j = bestsofar [ j ] | Start with the heaviest weight and emit index |
11,535 | def mappability ( args ) : p = OptionParser ( mappability . __doc__ ) p . add_option ( "--mer" , default = 50 , type = "int" , help = "User mer size" ) p . set_cpus ( ) opts , args = p . parse_args ( args ) if len ( args ) != 1 : sys . exit ( not p . print_help ( ) ) ref , = args K = opts . mer pf = ref . rsplit ( "." ... | %prog mappability reference . fasta |
11,536 | def freq ( args ) : p = OptionParser ( freq . __doc__ ) p . add_option ( "--mindepth" , default = 3 , type = "int" , help = "Minimum depth [default: %default]" ) p . add_option ( "--minqual" , default = 20 , type = "int" , help = "Minimum quality [default: %default]" ) p . set_outfile ( ) opts , args = p . parse_args (... | %prog freq fastafile bamfile |
11,537 | def frommaf ( args ) : p = OptionParser ( frommaf . __doc__ ) p . add_option ( "--validate" , help = "Validate coordinates against FASTA [default: %default]" ) opts , args = p . parse_args ( args ) if len ( args ) != 1 : sys . exit ( not p . print_help ( ) ) maf , = args snpfile = maf . rsplit ( "." , 1 ) [ 0 ] + ".vcf... | %prog frommaf maffile |
11,538 | def libs ( args ) : p = OptionParser ( libs . __doc__ ) p . set_db_opts ( dbname = "track" , credentials = None ) opts , args = p . parse_args ( args ) if len ( args ) != 1 : sys . exit ( not p . print_help ( ) ) libfile , = args sqlcmd = "select library.lib_id, library.name, bac.gb# from library join bac on " + "libra... | %prog libs libfile |
11,539 | def pull ( args ) : p = OptionParser ( pull . __doc__ ) p . set_db_opts ( dbname = "mtg2" , credentials = None ) p . add_option ( "--frag" , default = False , action = "store_true" , help = "The command to pull sequences from db [default: %default]" ) opts , args = p . parse_args ( args ) if len ( args ) != 1 : sys . e... | %prog pull libfile |
11,540 | def read_record ( fp , first_line = None ) : if first_line is None : first_line = fp . readline ( ) if not first_line : raise EOFError ( ) match = _START . match ( first_line ) if not match : raise Exception ( 'Bad start of message' , first_line ) type = match . group ( 1 ) message = Message ( type ) while True : row =... | Read a record from a file of AMOS messages |
11,541 | def filter ( args ) : p = OptionParser ( filter . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) != 2 : sys . exit ( not p . print_help ( ) ) frgfile , idsfile = args assert frgfile . endswith ( ".frg" ) fp = open ( idsfile ) allowed = set ( x . strip ( ) for x in fp ) logging . debug ( "A total of {0}... | %prog filter frgfile idsfile |
11,542 | def frg ( args ) : p = OptionParser ( frg . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) != 1 : sys . exit ( p . print_help ( ) ) frgfile , = args fastafile = frgfile . rsplit ( "." , 1 ) [ 0 ] + ".fasta" fp = open ( frgfile ) fw = open ( fastafile , "w" ) for rec in iter_records ( fp ) : if rec . ty... | %prog frg frgfile |
11,543 | def asm ( args ) : p = OptionParser ( asm . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) != 1 : sys . exit ( p . print_help ( ) ) asmfile , = args prefix = asmfile . rsplit ( "." , 1 ) [ 0 ] ctgfastafile = prefix + ".ctg.fasta" scffastafile = prefix + ".scf.fasta" fp = open ( asmfile ) ctgfw = open (... | %prog asm asmfile |
11,544 | def count ( args ) : p = OptionParser ( count . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) != 1 : sys . exit ( p . print_help ( ) ) frgfile , = args fp = open ( frgfile ) counts = defaultdict ( int ) for rec in iter_records ( fp ) : counts [ rec . type ] += 1 for type , cnt in sorted ( counts . ite... | %prog count frgfile |
11,545 | def prepare ( args ) : p = OptionParser ( prepare . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) != 2 : sys . exit ( not p . print_help ( ) ) counts , families = args countfiles = glob ( op . join ( counts , "*.count" ) ) countsdb = defaultdict ( list ) for c in countfiles : rs = RiceSample ( c ) cou... | %prog prepare countfolder families |
11,546 | def outlier_cutoff ( a , threshold = 3.5 ) : A = np . array ( a , dtype = float ) M = np . median ( A ) D = np . absolute ( A - M ) MAD = np . median ( D ) C = threshold / .67449 * MAD return M - C , M + C | Iglewicz and Hoaglin s robust returns the cutoff values - lower bound and upper bound . |
11,547 | def bed ( args ) : p = OptionParser ( bed . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) != 1 : sys . exit ( not p . print_help ( ) ) idsfile , = args ids = set ( x . strip ( ) for x in open ( idsfile ) ) data = get_bed_from_phytozome ( list ( ids ) ) pf = idsfile . rsplit ( "." , 1 ) [ 0 ] bedfile =... | %prog bed genes . ids |
11,548 | def bed ( args ) : p = OptionParser ( bed . __doc__ ) p . add_option ( "-o" , dest = "output" , default = "stdout" , help = "Output file name [default: %default]" ) p . add_option ( "--cutoff" , dest = "cutoff" , default = 10 , type = "int" , help = "Minimum read depth to report intervals [default: %default]" ) opts , ... | %prog bed binfile fastafile |
11,549 | def query ( args ) : p = OptionParser ( query . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) != 4 : sys . exit ( not p . print_help ( ) ) binfile , fastafile , ctgID , baseID = args b = BinFile ( binfile , fastafile ) ar = b . mmarray fastasize , sizes , offsets = get_offsets ( fastafile ) oi = offse... | %prog query binfile fastafile ctgID baseID |
11,550 | def count ( args ) : p = OptionParser ( count . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) != 2 : sys . exit ( not p . print_help ( ) ) coveragefile , fastafile = args countsfile = coveragefile . split ( "." ) [ 0 ] + ".bin" if op . exists ( countsfile ) : logging . error ( "`{0}` file exists. Remo... | %prog count t . coveragePerBase fastafile |
11,551 | def edges_to_path ( edges ) : if not edges : return None G = edges_to_graph ( edges ) path = nx . topological_sort ( G ) return path | Connect edges and return a path . |
11,552 | def max_sum ( a ) : max_sum , max_start_index , max_end_index = - Infinity , 0 , 0 current_max_sum = 0 current_start_index = 0 for current_end_index , x in enumerate ( a ) : current_max_sum += x if current_max_sum > max_sum : max_sum , max_start_index , max_end_index = current_max_sum , current_start_index , current_en... | For an input array a output the range that gives the largest sum |
11,553 | def silicosoma ( args ) : p = OptionParser ( silicosoma . __doc__ ) p . set_outfile ( ) opts , args = p . parse_args ( args ) if len ( args ) != 1 : sys . exit ( not p . print_help ( ) ) silicofile , = args fp = must_open ( silicofile ) fw = must_open ( opts . outfile , "w" ) next ( fp ) positions = [ int ( x ) for x i... | %prog silicosoma in . silico > out . soma |
11,554 | def condense ( args ) : from itertools import groupby from jcvi . assembly . patch import merge_ranges p = OptionParser ( condense . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) != 1 : sys . exit ( not p . print_help ( ) ) bedfile , = args bed = Bed ( bedfile , sorted = False ) key = lambda x : ( x .... | %prog condense OM . bed |
11,555 | def chimera ( args ) : p = OptionParser ( chimera . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) != 1 : sys . exit ( not p . print_help ( ) ) bedfile , = args bed = Bed ( bedfile ) selected = select_bed ( bed ) mapped = defaultdict ( set ) chimerabed = "chimera.bed" fw = open ( chimerabed , "w" ) for... | %prog chimera bedfile |
11,556 | def select_bed ( bed ) : ranges = [ Range ( x . seqid , x . start , x . end , float ( x . score ) , i ) for i , x in enumerate ( bed ) ] selected , score = range_chain ( ranges ) selected = [ bed [ x . id ] for x in selected ] return selected | Return non - overlapping set of ranges choosing high scoring blocks over low scoring alignments when there are conflicts . |
11,557 | def fasta ( args ) : from jcvi . formats . sizes import Sizes from jcvi . formats . agp import OO , build p = OptionParser ( fasta . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) != 3 : sys . exit ( not p . print_help ( ) ) bedfile , scffasta , pmolfasta = args pf = bedfile . rsplit ( "." , 1 ) [ 0 ] ... | %prog fasta bedfile scf . fasta pseudomolecules . fasta |
11,558 | def bed ( args ) : from jcvi . formats . bed import sort p = OptionParser ( bed . __doc__ ) p . add_option ( "--blockonly" , default = False , action = "store_true" , help = "Only print out large blocks, not fragments [default: %default]" ) p . add_option ( "--point" , default = False , action = "store_true" , help = "... | %prog bed xmlfile |
11,559 | def bam ( args ) : from jcvi . formats . sizes import Sizes from jcvi . formats . sam import index p = OptionParser ( bam . __doc__ ) p . set_home ( "eddyyeh" ) p . set_cpus ( ) opts , args = p . parse_args ( args ) if len ( args ) != 2 : sys . exit ( not p . print_help ( ) ) gsnapfile , fastafile = args EYHOME = opts ... | %prog snp input . gsnap ref . fasta |
11,560 | def index ( args ) : p = OptionParser ( index . __doc__ ) p . add_option ( "--supercat" , default = False , action = "store_true" , help = "Concatenate reference to speed up alignment" ) opts , args = p . parse_args ( args ) if len ( args ) != 1 : sys . exit ( not p . print_help ( ) ) dbfile , = args check_index ( dbfi... | %prog index database . fasta Wrapper for gmap_build . Same interface . |
11,561 | def gmap ( args ) : p = OptionParser ( gmap . __doc__ ) p . add_option ( "--cross" , default = False , action = "store_true" , help = "Cross-species alignment" ) p . add_option ( "--npaths" , default = 0 , type = "int" , help = "Maximum number of paths to show." " If set to 0, prints two paths if chimera" " detected, e... | %prog gmap database . fasta fastafile |
11,562 | def align ( args ) : from jcvi . formats . fastq import guessoffset p = OptionParser ( align . __doc__ ) p . add_option ( "--rnaseq" , default = False , action = "store_true" , help = "Input is RNA-seq reads, turn splicing on" ) p . add_option ( "--native" , default = False , action = "store_true" , help = "Convert GSN... | %prog align database . fasta read1 . fq read2 . fq |
11,563 | def get_1D_overlap ( eclusters , depth = 1 ) : overlap_set = set ( ) active = set ( ) ends = [ ] for i , ( chr , left , right ) in enumerate ( eclusters ) : ends . append ( ( chr , left , 0 , i ) ) ends . append ( ( chr , right , 1 , i ) ) ends . sort ( ) chr_last = "" for chr , pos , left_right , i in ends : if chr !=... | Find blocks that are 1D overlapping returns cliques of block ids that are in conflict |
11,564 | def make_range ( clusters , extend = 0 ) : eclusters = [ ] for cluster in clusters : xlist , ylist , scores = zip ( * cluster ) score = _score ( cluster ) xchr , xmin = min ( xlist ) xchr , xmax = max ( xlist ) ychr , ymin = min ( ylist ) ychr , ymax = max ( ylist ) xmax += extend ymax += extend if xmax < xmin : xmin ,... | Convert to interval ends from a list of anchors extend modifies the xmax ymax boundary of the box which can be positive or negative very useful when we want to make the range as fuzzy as we specify |
11,565 | def get_constraints ( clusters , quota = ( 1 , 1 ) , Nmax = 0 ) : qa , qb = quota eclusters = make_range ( clusters , extend = - Nmax ) nodes = [ ( i + 1 , c [ - 1 ] ) for i , c in enumerate ( eclusters ) ] eclusters_x , eclusters_y , scores = zip ( * eclusters ) constraints_x = get_1D_overlap ( eclusters_x , qa ) cons... | Check pairwise cluster comparison if they overlap then mark edge as conflict |
11,566 | def format_lp ( nodes , constraints_x , qa , constraints_y , qb ) : lp_handle = cStringIO . StringIO ( ) lp_handle . write ( "Maximize\n " ) records = 0 for i , score in nodes : lp_handle . write ( "+ %d x%d " % ( score , i ) ) records += 1 if records % 10 == 0 : lp_handle . write ( "\n" ) lp_handle . write ( "\n" ) nu... | Maximize 4 x1 + 2 x2 + 3 x3 + x4 Subject To x1 + x2 < = 1 End |
11,567 | def solve_lp ( clusters , quota , work_dir = "work" , Nmax = 0 , self_match = False , solver = "SCIP" , verbose = False ) : qb , qa = quota nodes , constraints_x , constraints_y = get_constraints ( clusters , ( qa , qb ) , Nmax = Nmax ) if self_match : constraints_x = constraints_y = constraints_x | constraints_y lp_da... | Solve the formatted LP instance |
11,568 | def print_maps_by_type ( map_type , number = None ) : map_type = map_type . lower ( ) . capitalize ( ) if map_type not in MAP_TYPES : s = 'Invalid map type, must be one of {0}' . format ( MAP_TYPES ) raise ValueError ( s ) print ( map_type ) map_keys = sorted ( COLOR_MAPS [ map_type ] . keys ( ) ) format_str = '{0:8} ... | Print all available maps of a given type . |
11,569 | def get_map ( name , map_type , number , reverse = False ) : number = str ( number ) map_type = map_type . lower ( ) . capitalize ( ) if map_type not in MAP_TYPES : s = 'Invalid map type, must be one of {0}' . format ( MAP_TYPES ) raise ValueError ( s ) map_names = dict ( ( k . lower ( ) , k ) for k in COLOR_MAPS [ map... | Return a BrewerMap representation of the specified color map . |
11,570 | def _load_maps_by_type ( map_type ) : seq_maps = COLOR_MAPS [ map_type ] loaded_maps = { } for map_name in seq_maps : loaded_maps [ map_name ] = { } for num in seq_maps [ map_name ] : inum = int ( num ) colors = seq_maps [ map_name ] [ num ] [ 'Colors' ] bmap = BrewerMap ( map_name , map_type , colors ) loaded_maps [ m... | Load all maps of a given type into a dictionary . |
11,571 | def mpl_colors ( self ) : mc = [ ] for color in self . colors : mc . append ( tuple ( [ x / 255. for x in color ] ) ) return mc | Colors expressed on the range 0 - 1 as used by matplotlib . |
11,572 | def get_mpl_colormap ( self , ** kwargs ) : if not HAVE_MPL : raise RuntimeError ( 'matplotlib not available.' ) cmap = LinearSegmentedColormap . from_list ( self . name , self . mpl_colors , ** kwargs ) return cmap | A color map that can be used in matplotlib plots . Requires matplotlib to be importable . Keyword arguments are passed to matplotlib . colors . LinearSegmentedColormap . from_list . |
11,573 | def show_as_blocks ( self , block_size = 100 ) : from ipythonblocks import BlockGrid grid = BlockGrid ( self . number , 1 , block_size = block_size ) for block , color in zip ( grid , self . colors ) : block . rgb = color grid . show ( ) | Show colors in the IPython Notebook using ipythonblocks . |
11,574 | def colorbrewer2_url ( self ) : url = 'http://colorbrewer2.org/index.html?type={0}&scheme={1}&n={2}' return url . format ( self . type . lower ( ) , self . name , self . number ) | URL that can be used to view the color map at colorbrewer2 . org . |
11,575 | def summary ( args ) : from jcvi . formats . fasta import summary as fsummary from jcvi . utils . cbook import percentage , human_size p = OptionParser ( summary . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) != 3 : sys . exit ( not p . print_help ( ) ) chainfile , oldfasta , newfasta = args chain = ... | %prog summary old . new . chain old . fasta new . fasta |
11,576 | def fromagp ( args ) : from jcvi . formats . agp import AGP from jcvi . formats . sizes import Sizes p = OptionParser ( fromagp . __doc__ ) p . add_option ( "--novalidate" , default = False , action = "store_true" , help = "Do not validate AGP" ) opts , args = p . parse_args ( args ) if len ( args ) != 3 : sys . exit (... | %prog fromagp agpfile componentfasta objectfasta |
11,577 | def blat ( args ) : p = OptionParser ( blat . __doc__ ) p . add_option ( "--minscore" , default = 100 , type = "int" , help = "Matches minus mismatches gap penalty [default: %default]" ) p . add_option ( "--minid" , default = 98 , type = "int" , help = "Minimum sequence identity [default: %default]" ) p . set_cpus ( ) ... | %prog blat old . fasta new . fasta |
11,578 | def frompsl ( args ) : from jcvi . formats . sizes import Sizes p = OptionParser ( frompsl . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) != 3 : sys . exit ( not p . print_help ( ) ) pslfile , oldfasta , newfasta = args pf = oldfasta . split ( "." ) [ 0 ] chainfile = pf + ".chain" twobitfiles = [ ] f... | %prog frompsl old . new . psl old . fasta new . fasta |
11,579 | def lastz_to_blast ( row ) : atoms = row . strip ( ) . split ( "\t" ) name1 , name2 , coverage , identity , nmismatch , ngap , start1 , end1 , strand1 , start2 , end2 , strand2 , score = atoms identity = identity . replace ( "%" , "" ) hitlen = coverage . split ( "/" ) [ 1 ] score = float ( score ) same_strand = ( stra... | Convert the lastz tabular to the blast tabular see headers above Obsolete after LASTZ version 1 . 02 . 40 |
11,580 | def lastz_2bit ( t ) : bfasta_fn , afasta_fn , outfile , lastz_bin , extra , mask , format = t ref_tags = [ Darkspace ] qry_tags = [ Darkspace ] ref_tags , qry_tags = add_mask ( ref_tags , qry_tags , mask = mask ) lastz_cmd = Lastz_template . format ( lastz_bin , bfasta_fn , ref_tags , afasta_fn , qry_tags ) if extra :... | Used for formats other than BLAST i . e . lav maf etc . which requires the database file to contain a single FASTA record . |
11,581 | def augustus ( args ) : p = OptionParser ( augustus . __doc__ ) p . add_option ( "--species" , default = "maize" , help = "Use species model for prediction" ) p . add_option ( "--hintsfile" , help = "Hint-guided AUGUSTUS" ) p . add_option ( "--nogff3" , default = False , action = "store_true" , help = "Turn --gff3=off"... | %prog augustus fastafile |
11,582 | def star ( args ) : p = OptionParser ( star . __doc__ ) p . add_option ( "--single" , default = False , action = "store_true" , help = "Single end mapping" ) p . set_fastq_names ( ) p . set_cpus ( ) opts , args = p . parse_args ( args ) if len ( args ) != 2 : sys . exit ( not p . print_help ( ) ) folder , reference = a... | %prog star folder reference |
11,583 | def cufflinks ( args ) : p = OptionParser ( cufflinks . __doc__ ) p . add_option ( "--gtf" , help = "Reference annotation [default: %default]" ) p . set_cpus ( ) opts , args = p . parse_args ( args ) if len ( args ) != 2 : sys . exit ( not p . print_help ( ) ) folder , reference = args cpus = opts . cpus gtf = opts . g... | %prog cufflinks folder reference |
11,584 | def tophat ( args ) : from jcvi . apps . bowtie import check_index from jcvi . formats . fastq import guessoffset p = OptionParser ( tophat . __doc__ ) p . add_option ( "--gtf" , help = "Reference annotation [default: %default]" ) p . add_option ( "--single" , default = False , action = "store_true" , help = "Single en... | %prog tophat folder reference |
11,585 | def hmean_int ( a , a_min = 5778 , a_max = 1149851 ) : from scipy . stats import hmean return int ( round ( hmean ( np . clip ( a , a_min , a_max ) ) ) ) | Harmonic mean of an array returns the closest int |
11,586 | def golden_array ( a , phi = 1.61803398875 , lb = LB , ub = UB ) : counts = np . zeros ( BB , dtype = int ) for x in a : c = int ( round ( math . log ( x , phi ) ) ) if c < lb : c = lb if c > ub : c = ub counts [ c - lb ] += 1 return counts | Given list of ints we aggregate similar values so that it becomes an array of multiples of phi where phi is the golden ratio . |
11,587 | def heatmap ( args ) : p = OptionParser ( heatmap . __doc__ ) p . add_option ( "--resolution" , default = 500000 , type = "int" , help = "Resolution when counting the links" ) p . add_option ( "--chr" , help = "Plot this contig/chr only" ) p . add_option ( "--nobreaks" , default = False , action = "store_true" , help =... | %prog heatmap input . npy genome . json |
11,588 | def get_seqstarts ( bamfile , N ) : import pysam bamfile = pysam . AlignmentFile ( bamfile , "rb" ) seqsize = { } for kv in bamfile . header [ "SQ" ] : if kv [ "LN" ] < 10 * N : continue seqsize [ kv [ "SN" ] ] = kv [ "LN" ] / N + 1 allseqs = natsorted ( seqsize . keys ( ) ) allseqsizes = np . array ( [ seqsize [ x ] f... | Go through the SQ headers and pull out all sequences with size greater than the resolution settings i . e . contains at least a few cells |
11,589 | def get_distbins ( start = 100 , bins = 2500 , ratio = 1.01 ) : b = np . ones ( bins , dtype = "float64" ) b [ 0 ] = 100 for i in range ( 1 , bins ) : b [ i ] = b [ i - 1 ] * ratio bins = np . around ( b ) . astype ( dtype = "int" ) binsizes = np . diff ( bins ) return bins , binsizes | Get exponentially sized |
11,590 | def simulate ( args ) : p = OptionParser ( simulate . __doc__ ) p . add_option ( "--genomesize" , default = 10000000 , type = "int" , help = "Genome size" ) p . add_option ( "--genes" , default = 1000 , type = "int" , help = "Number of genes" ) p . add_option ( "--contigs" , default = 100 , type = "int" , help = "Numbe... | %prog simulate test |
11,591 | def write_last_and_beds ( pf , GenePositions , ContigStarts ) : qbedfile = pf + "tigs.bed" sbedfile = pf + "chr.bed" lastfile = "{}tigs.{}chr.last" . format ( pf , pf ) qbedfw = open ( qbedfile , "w" ) sbedfw = open ( sbedfile , "w" ) lastfw = open ( lastfile , "w" ) GeneContigs = np . searchsorted ( ContigStarts , Gen... | Write LAST file query and subject BED files . |
11,592 | def write_clm ( pf , ICLinkStartContigs , ICLinkEndContigs , ICLinkStarts , ICLinkEnds , ContigStarts , ContigSizes ) : clm = defaultdict ( list ) for start , end , linkstart , linkend in zip ( ICLinkStartContigs , ICLinkEndContigs , ICLinkStarts , ICLinkEnds ) : start_a = ContigStarts [ start ] start_b = start_a + Con... | Write CLM file from simulated data . |
11,593 | def density ( args ) : p = OptionParser ( density . __doc__ ) p . add_option ( "--save" , default = False , action = "store_true" , help = "Write log densitites of contigs to file" ) p . set_cpus ( ) opts , args = p . parse_args ( args ) if len ( args ) != 1 : sys . exit ( not p . print_help ( ) ) clmfile , = args clm ... | %prog density test . clm |
11,594 | def optimize ( args ) : p = OptionParser ( optimize . __doc__ ) p . add_option ( "--skiprecover" , default = False , action = "store_true" , help = "Do not import 'recover' contigs" ) p . add_option ( "--startover" , default = False , action = "store_true" , help = "Do not resume from existing tour file" ) p . add_opti... | %prog optimize test . clm |
11,595 | def optimize_orientations ( fwtour , clm , phase , cpus ) : tour_contigs = clm . active_contigs tour = clm . tour oo = clm . oo print_tour ( fwtour , tour , "FLIPALL{}" . format ( phase ) , tour_contigs , oo , signs = clm . signs ) tag1 = clm . flip_whole ( tour ) print_tour ( fwtour , tour , "FLIPWHOLE{}" . format ( p... | Optimize the orientations of contigs by using heuristic flipping . |
11,596 | def iter_last_tour ( tourfile , clm ) : row = open ( tourfile ) . readlines ( ) [ - 1 ] _tour , _tour_o = separate_tour_and_o ( row ) tour = [ ] tour_o = [ ] for tc , to in zip ( _tour , _tour_o ) : if tc not in clm . contigs : logging . debug ( "Contig `{}` in file `{}` not found in `{}`" . format ( tc , tourfile , cl... | Extract last tour from tourfile . The clm instance is also passed in to see if any contig is covered in the clm . |
11,597 | def iter_tours ( tourfile , frames = 1 ) : fp = open ( tourfile ) i = 0 for row in fp : if row [ 0 ] == '>' : label = row [ 1 : ] . strip ( ) if label . startswith ( "GA" ) : pf , j , score = label . split ( "-" , 2 ) j = int ( j ) else : j = 0 i += 1 else : if j % frames != 0 : continue tour , tour_o = separate_tour_a... | Extract tours from tourfile . Tourfile contains a set of contig configurations generated at each iteration of the genetic algorithm . Each configuration has two rows first row contains iteration id and score second row contains list of contigs separated by comma . |
11,598 | def movie ( args ) : p = OptionParser ( movie . __doc__ ) p . add_option ( "--frames" , default = 500 , type = "int" , help = "Only plot every N frames" ) p . add_option ( "--engine" , default = "ffmpeg" , choices = ( "ffmpeg" , "gifsicle" ) , help = "Movie engine, output MP4 or GIF" ) p . set_beds ( ) opts , args , io... | %prog movie test . tour test . clm ref . contigs . last |
11,599 | def prepare_ec ( oo , sizes , M ) : tour = range ( len ( oo ) ) tour_sizes = np . array ( [ sizes . sizes [ x ] for x in oo ] ) tour_M = M [ oo , : ] [ : , oo ] return tour , tour_sizes , tour_M | This prepares EC and converts from contig_id to an index . |
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