Module Expr Str ImportFrom alias ImportFrom alias ImportFrom alias alias Import alias identifier ClassDef bases body FunctionDef arguments args NameParam defaults body Pass decorator_list decorator_list ClassDef bases body Expr Str FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults NameLoad Num Num body Assign AttributeStore NameLoad attr Call NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr ListLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad With Call NameLoad AttributeLoad NameLoad attr NameStore body For NameStore NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad NameLoad attr If CompareIsNot NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad body Expr Str Return Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad body Expr Str Return Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Expr Str With Call NameLoad NameLoad NameStore body Assign NameStore ListComp SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr Index Num comprehension NameStore NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Expr Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AugAssignAdd AttributeStore NameLoad attr NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str For NameStore NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Delete SubscriptDel AttributeLoad AttributeLoad NameLoad attr attr Index NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults body Expr Str Assign NameStore BinOpAdd Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Num Assign NameStore BinOpAdd Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Num Assign NameStore BinOpAdd Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Str Num Assign NameStore BinOpSub BinOpSub BinOpSub Num NameLoad NameLoad NameLoad Assign NameStore CompareLtE NameLoad Num Assign SubscriptStore NameLoad Index Call AttributeLoad NameLoad attr Num Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr BinOpDiv Num Num Assign NameStore NameLoad Assign NameStore Num For NameStore NameLoad body If CompareEq NameLoad Str body AugAssignAdd NameStore SubscriptLoad NameLoad Index NameLoad AugAssignAdd NameStore Num orelse If CompareEq NameLoad Str body AugAssignAdd NameStore BinOpAdd SubscriptLoad NameLoad Index NameLoad NameLoad AugAssignAdd NameStore Num orelse If CompareEq NameLoad Str body AugAssignAdd NameStore BinOpAdd SubscriptLoad NameLoad Index NameLoad NameLoad AugAssignAdd NameStore Num orelse AugAssignAdd NameStore SubscriptLoad NameLoad Index NameLoad Assert CompareEq NameLoad NameLoad Return NameLoad decorator_list decorator_list ClassDef bases body Expr Str FunctionDef arguments args NameParam NameParam NameParam NameParam defaults Num Num body Assign AttributeStore NameLoad attr Call NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr ListLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad body Expr Str Return Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad body Expr Str Return Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Expr Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign NameStore ListComp SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr Index Num comprehension NameStore Call NameLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str For NameStore NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Delete SubscriptDel AttributeLoad AttributeLoad NameLoad attr attr Index NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults body Expr Str Assign NameStore BinOpAdd Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad Num Assign NameStore BinOpSub Num NameLoad Assign NameStore CompareLtE NameLoad Num Assign SubscriptStore NameLoad Index Call AttributeLoad NameLoad attr Num Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr BinOpDiv Num Num Assign NameStore NameLoad Assign NameStore Num For NameStore NameLoad body If CompareEq NameLoad Str body AugAssignAdd NameStore SubscriptLoad NameLoad Index NameLoad AugAssignAdd NameStore Num orelse If CompareEq NameLoad Str body AugAssignAdd NameStore BinOpAdd SubscriptLoad NameLoad Index NameLoad NameLoad AugAssignAdd NameStore Num orelse If CompareEq NameLoad Str body AugAssignAdd NameStore BinOpAdd SubscriptLoad NameLoad Index NameLoad NameLoad AugAssignAdd NameStore Num orelse AugAssignAdd NameStore SubscriptLoad NameLoad Index NameLoad Assert CompareEq NameLoad NameLoad Return NameLoad decorator_list decorator_list ClassDef bases body Expr Str FunctionDef arguments args NameParam defaults body Pass decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad body Expr Str Return Num decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad body Expr Str Return Num decorator_list decorator_list ClassDef bases body Expr Str FunctionDef arguments args NameParam NameParam NameParam NameParam defaults body Assign AttributeStore NameLoad attr Call NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr BinOpSub BinOpSub BinOpSub Num NameLoad NameLoad NameLoad Assert CompareGt AttributeLoad NameLoad attr Num decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Expr Str Pass decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str Pass decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad body Expr Str Return Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad body Expr Str Return Call AttributeLoad AttributeLoad NameLoad attr attr keyword NameLoad keyword NameLoad keyword NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults body Expr Str Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Num For NameStore NameLoad body If CompareEq NameLoad Str body AugAssignAdd NameStore NameLoad orelse If CompareEq NameLoad Str body AugAssignAdd NameStore NameLoad orelse If CompareEq NameLoad Str body AugAssignAdd NameStore NameLoad orelse AugAssignAdd NameStore NameLoad Return NameLoad decorator_list decorator_list
N/A N/A Define Probability Models, including ProbFromQV and ProbFromModel. pbcore.io.FastaIO FastaReader pbcore.io.FastqIO FastqReader pbtools.pbtranscript.io.BasQV basQVcacher fastqQVcacher N/A numpy np aloha N/A N/A __init__ N/A N/A self N/A N/A N/A N/A N/A ProbFromQV N/A N/A N/A 
    Probability model constructed from FOFN files using
    quality values.
     __init__ N/A N/A self input_fofn fasta_filename prob_threshold window_size N/A None 0.03 5 N/A N/A N/A self qver N/A basQVcacher N/A N/A self input_fofn input_fofn N/A N/A self seqids N/A N/A N/A self prob_threshold prob_threshold N/A N/A self window_size window_size N/A N/A self full_prob None N/A N/A open N/A self input_fofn f N/A N/A line f N/A N/A N/A N/A N/A self qver add_bash5 N/A N/A line strip N/A N/A fasta_filename None N/A N/A N/A N/A self add_seqs_from_fasta fasta_filename N/A get_smoothed N/A N/A self qID qvname position N/A None N/A N/A 
        Get smoothed QV of read=qID, type=qvname, position=position.
         N/A N/A N/A N/A self qver get_smoothed qID qvname position N/A get N/A N/A self qID qvname position N/A None N/A N/A 
        Get QV of read=qID, type=qvname, position=position.
         N/A N/A N/A N/A self qver get qID qvname position N/A add_seqs_from_fasta N/A N/A self fasta_filename smooth N/A True N/A N/A Add sequence ids from a fasta file. N/A N/A FastaReader fasta_filename reader N/A N/A newids N/A N/A N/A N/A N/A r name split N/A 0 N/A r reader N/A N/A N/A self add_ids_from_fasta newids smooth N/A add_ids_from_fasta N/A N/A self newids _smooth N/A True N/A N/A Add sequence ids. N/A N/A N/A N/A self qver precache newids N/A N/A self seqids newids N/A N/A N/A N/A self qver presmooth newids N/A self window_size N/A remove_ids N/A N/A self ids N/A N/A N/A Remove ids from self.seqids. N/A _id ids N/A N/A N/A N/A N/A self seqids remove _id N/A N/A N/A N/A self qver qv N/A _id N/A calc_prob_from_aln N/A N/A self qID qStart qEnd fakecigar N/A N/A N/A 
        aln_record is a pysam.AlignedRead
         N/A prob_sub N/A N/A N/A N/A self qver get qID SubstitutionQV 0.0001 N/A prob_ins N/A N/A N/A N/A self qver get qID InsertionQV 0.0001 N/A prob_del N/A N/A N/A N/A self qver get qID DeletionQV 0.0001 N/A prob_mat N/A N/A N/A 1 prob_sub prob_ins prob_del N/A ii N/A prob_mat 0 N/A N/A prob_mat N/A N/A N/A ii nonzero 0.001 N/A prob_sub N/A N/A np log prob_sub N/A prob_ins N/A N/A np log prob_ins N/A prob_del N/A N/A np log prob_del N/A prob_mat N/A N/A np log prob_mat N/A one_three N/A N/A np log N/A 1 3.0 N/A cur_q_pos qStart N/A score 0 N/A x fakecigar N/A N/A N/A x M N/A N/A score N/A prob_mat N/A cur_q_pos N/A cur_q_pos 1 N/A N/A N/A x S N/A N/A score N/A N/A prob_sub N/A cur_q_pos one_three N/A cur_q_pos 1 N/A N/A N/A x I N/A N/A score N/A N/A prob_ins N/A cur_q_pos one_three N/A cur_q_pos 1 N/A N/A score N/A prob_del N/A cur_q_pos N/A N/A cur_q_pos qEnd N/A score N/A N/A ProbFromFastq N/A N/A N/A 
    Probability model constructed from Fastq files using a single QV for everything
     __init__ N/A N/A self fastq_filename prob_threshold window_size N/A 0.03 5 N/A N/A N/A self qver N/A fastqQVcacher N/A N/A self fastq_filename fastq_filename N/A N/A self seqids N/A N/A N/A self prob_threshold prob_threshold N/A N/A self window_size window_size N/A N/A self full_prob None N/A N/A N/A self add_seqs_from_fastq fastq_filename N/A get_smoothed N/A N/A self qID qvname position N/A None N/A N/A 
        Get smoothed QV of read=qID, type=qvname, position=position.
        In reality, qvname is ignored.
         N/A N/A N/A N/A self qver get_smoothed qID qvname position N/A get N/A N/A self qID qvname position N/A None N/A N/A 
        Get QV of read=qID, type=qvname, position=position.
        In reality, qvname is ignored.
         N/A N/A N/A N/A self qver get qID qvname position N/A add_seqs_from_fastq N/A N/A self fastq_filename smooth N/A True N/A N/A Add sequence ids from a fastq file. N/A N/A N/A N/A self qver precache_fastq fastq_filename N/A newids N/A N/A N/A N/A N/A r name split N/A 0 N/A r N/A FastqReader fastq_filename N/A N/A N/A N/A self qver presmooth newids N/A self window_size N/A remove_ids N/A N/A self ids N/A N/A N/A Remove ids from self.seqids. N/A _id ids N/A N/A N/A N/A N/A self seqids remove _id N/A N/A N/A N/A self qver qv N/A _id N/A calc_prob_from_aln N/A N/A self qID qStart qEnd fakecigar N/A N/A N/A 
        aln_record is a pysam.AlignedRead
         N/A prob_err N/A N/A N/A N/A self qver get qID None 0.0001 N/A prob_mat N/A 1 prob_err N/A ii N/A prob_mat 0 N/A N/A prob_mat N/A N/A N/A ii nonzero 0.001 N/A prob_err N/A N/A np log prob_err N/A prob_mat N/A N/A np log prob_mat N/A one_three N/A N/A np log N/A 1 3.0 N/A cur_q_pos qStart N/A score 0 N/A x fakecigar N/A N/A N/A x M N/A N/A score N/A prob_mat N/A cur_q_pos N/A cur_q_pos 1 N/A N/A N/A x S N/A N/A score N/A N/A prob_err N/A cur_q_pos one_three N/A cur_q_pos 1 N/A N/A N/A x I N/A N/A score N/A N/A prob_err N/A cur_q_pos one_three N/A cur_q_pos 1 N/A N/A score N/A prob_err N/A cur_q_pos N/A N/A cur_q_pos qEnd N/A score N/A N/A fakeQVer N/A N/A N/A 
    Used by ProbFromModel to support the fake .get and .getsmoothed
     __init__ N/A N/A self N/A N/A N/A N/A get N/A N/A self _x _y _z N/A None N/A N/A Fake get(). N/A 0.0 N/A get_smoothed N/A N/A self qID qvname position N/A None N/A N/A Fake get_smoothed. N/A 0.0 N/A N/A ProbFromModel N/A N/A N/A Probability model from fixed indel/substitution rates. __init__ N/A N/A self r_mis r_ins r_del N/A N/A N/A N/A self qver N/A fakeQVer N/A N/A self r_mis r_mis N/A N/A self r_ins r_ins N/A N/A self r_del r_del N/A N/A self r_mat N/A N/A N/A 1 r_mis r_ins r_del N/A N/A N/A self r_mat 0 N/A add_seqs_from_fasta N/A N/A self fasta_filename smooth N/A True N/A N/A # dummy, nothing to do N/A N/A remove_ids N/A N/A self ids N/A N/A N/A # dummy, nothing to do N/A N/A get N/A N/A self x y z N/A None N/A N/A Return QV for x, y, z. N/A N/A N/A N/A self qver get x y z N/A get_smoothed N/A N/A self qID qvname position N/A None N/A N/A Get smoothed QV for qId, qvname, position. N/A N/A N/A N/A self qver get_smoothed qID qID qvname qvname position position N/A calc_prob_from_aln N/A N/A self _qID _qStart _qEnd fakecigar N/A N/A N/A Calculate probability from an alingment. N/A prob_mat N/A N/A np log N/A self r_mat N/A prob_sub N/A N/A np log N/A self r_mis N/A prob_ins N/A N/A np log N/A self r_ins N/A prob_del N/A N/A np log N/A self r_del N/A score 0 N/A x fakecigar N/A N/A N/A x M N/A N/A score prob_mat N/A N/A N/A x S N/A N/A score prob_sub N/A N/A N/A x I N/A N/A score prob_ins N/A N/A score prob_del N/A score N/A N/A