Module ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr Dict Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults body If UnaryOpNot CompareIn NameLoad AttributeLoad NameLoad attr body Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad Dict Assign NameStore BinOpDiv NameLoad Num If UnaryOpNot CompareIn NameLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad body Assign SubscriptStore SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Index NameLoad ListLoad Expr Call AttributeLoad SubscriptLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Index NameLoad attr Num TupleLoad NameLoad NameLoad NameLoad If CompareNotEq BinOpDiv NameLoad Num NameLoad body For NameStore Call NameLoad BinOpAdd NameLoad Num BinOpAdd BinOpDiv NameLoad Num Num body If UnaryOpNot CompareIn NameLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad body Assign SubscriptStore SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Index NameLoad ListLoad Expr Call AttributeLoad SubscriptLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Index NameLoad attr Num TupleLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults NameLoad body Expr Str If UnaryOpNot CompareIn NameLoad AttributeLoad NameLoad attr body Return TupleLoad NameLoad NameLoad Assign NameStore BinOpDiv NameLoad Num If UnaryOpNot CompareIn NameLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad body Return TupleLoad NameLoad NameLoad For TupleStore NameStore NameStore NameStore SubscriptLoad SubscriptLoad AttributeLoad NameLoad attr Index NameLoad Index NameLoad body If BoolOpAnd CompareGtE NameLoad NameLoad CompareLtE NameLoad NameLoad body If BoolOpOr NameLoad CompareEq NameLoad NameLoad body Return TupleLoad AttributeLoad NameLoad attr NameLoad Return TupleLoad AttributeLoad NameLoad attr NameLoad Return TupleLoad NameLoad NameLoad decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad NameLoad body Assign AttributeStore NameLoad attr ListLoad Assign AttributeStore NameLoad attr Dict Assign AttributeStore NameLoad attr NameLoad Assign NameStore Call NameLoad Str Assign NameStore Call NameLoad Str Assign NameStore Call NameLoad Str Assign NameStore Call NameLoad Str Assign NameStore Call NameLoad Str Assign NameStore Call NameLoad Str For NameStore AttributeLoad NameLoad attr body If BoolOpAnd NameLoad UnaryOpNot CompareIn AttributeLoad NameLoad attr NameLoad body Continue If CompareEq AttributeLoad NameLoad attr Str body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr BinOpSub AttributeLoad NameLoad attr Num AttributeLoad NameLoad attr orelse Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr BinOpAdd AttributeLoad NameLoad attr Num For NameStore AttributeLoad NameLoad attr body If AttributeLoad NameLoad attr body For TupleStore NameStore NameStore AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad NameLoad For TupleStore NameStore NameStore AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad NameLoad For TupleStore NameStore NameStore AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore NameLoad For TupleStore NameStore NameStore AttributeLoad NameLoad attr body If NameLoad body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num Assign SubscriptStore AttributeLoad NameLoad attr Index Str Num decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body If AttributeLoad NameLoad attr body Return If BoolOpAnd AttributeLoad NameLoad attr AttributeLoad NameLoad attr UnaryOpNot AttributeLoad NameLoad attr body Return Assign NameStore NameLoad Assign NameStore NameLoad Assign NameStore IfExp AttributeLoad NameLoad attr Str Str If CompareEq NameLoad Str body Assign NameStore Str If UnaryOpNot NameLoad body For TupleStore NameStore NameStore AttributeLoad NameLoad attr body If CompareEq NameLoad Num body Assign NameStore Str Break If UnaryOpNot NameLoad body For NameStore AttributeLoad NameLoad attr body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad AttributeLoad NameLoad attr If NameLoad body Break If UnaryOpNot NameLoad body Assign NameStore Str If NameLoad body If NameLoad body AugAssignAdd SubscriptStore AttributeLoad NameLoad attr Index BinOpMod Str NameLoad Num orelse AugAssignAdd SubscriptStore AttributeLoad NameLoad attr Index NameLoad Num Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults body Assign NameStore NameLoad Assign NameStore NameLoad If BoolOpOr CompareEq NameLoad Str CompareEq NameLoad Str body Assign NameStore Str If UnaryOpNot NameLoad body For NameStore AttributeLoad NameLoad attr body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad If NameLoad body Assign NameStore BinOpMod Str NameLoad If CompareNotEq NameLoad NameLoad body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad If NameLoad body Assign NameStore BinOpMod Str NameLoad If BoolOpAnd NameLoad NameLoad CompareNotEq NameLoad NameLoad body Assign NameStore BinOpMod Str TupleLoad NameLoad NameLoad If UnaryOpNot NameLoad body Assign NameStore Str decorator_list decorator_list
N/A RangeMatch N/A object N/A N/A 
    Simple genomic ranges.  You can define chrom:start-end ranges, then ask if a
    particular genomic coordinate maps to any of those ranges.  This is less-
    efficient than an R-Tree, but easier to code.
     __init__ N/A N/A self name N/A N/A N/A N/A self ranges N/A N/A N/A self name name N/A add_range N/A N/A self chrom strand start end N/A N/A N/A N/A N/A chrom N/A self ranges N/A N/A N/A N/A self ranges N/A chrom N/A N/A bin N/A start 100000 N/A N/A N/A bin N/A N/A self ranges N/A chrom N/A N/A N/A N/A N/A self ranges N/A chrom N/A bin N/A N/A N/A N/A N/A N/A N/A self ranges N/A chrom N/A bin insert 0 N/A start end strand N/A N/A N/A end 100000 bin N/A N/A bin N/A xrange N/A bin 1 N/A N/A end 100000 1 N/A N/A N/A N/A bin N/A N/A self ranges N/A chrom N/A N/A N/A N/A N/A self ranges N/A chrom N/A bin N/A N/A N/A N/A N/A N/A N/A self ranges N/A chrom N/A bin insert 0 N/A start end strand N/A get_tag N/A N/A self chrom strand pos ignore_strand N/A False N/A N/A 
        returns (region, is_reverse_orientation)
         N/A N/A N/A chrom N/A self ranges N/A N/A N/A None False N/A bin N/A pos 100000 N/A N/A N/A bin N/A N/A self ranges N/A chrom N/A N/A N/A None False N/A N/A start end r_strand N/A N/A N/A self ranges N/A chrom N/A bin N/A N/A N/A N/A pos start N/A pos end N/A N/A N/A ignore_strand N/A strand r_strand N/A N/A N/A N/A self name False N/A N/A N/A self name True N/A N/A None False N/A N/A RegionTagger N/A object N/A __init__ N/A N/A self gtf valid_chroms only_first_fragment N/A None True N/A N/A N/A self regions N/A N/A N/A self counts N/A N/A N/A self only_first_fragment only_first_fragment N/A coding N/A RangeMatch coding N/A exons N/A RangeMatch other-exon N/A utr_5 N/A RangeMatch utr-5 N/A utr_3 N/A RangeMatch utr-3 N/A introns N/A RangeMatch intron N/A promoters N/A RangeMatch promoter N/A gene N/A gtf genes N/A N/A N/A valid_chroms N/A N/A N/A gene chrom valid_chroms N/A N/A N/A N/A N/A gene strand + N/A N/A N/A N/A promoters add_range N/A gene chrom N/A gene strand N/A N/A gene start 2000 N/A gene start N/A N/A N/A N/A promoters add_range N/A gene chrom N/A gene strand N/A gene end N/A N/A gene end 2000 N/A transcript N/A gene transcripts N/A N/A N/A transcript has_cds N/A N/A N/A start end N/A transcript cds N/A N/A N/A N/A coding add_range N/A gene chrom N/A gene strand start end N/A N/A s e N/A transcript utr_5 N/A N/A N/A N/A utr_5 add_range N/A gene chrom N/A gene strand s e N/A N/A s e N/A transcript utr_3 N/A N/A N/A N/A utr_3 add_range N/A gene chrom N/A gene strand s e N/A last_end None N/A N/A start end N/A transcript exons N/A N/A last_end N/A N/A N/A N/A introns add_range N/A gene chrom N/A gene strand last_end start N/A N/A N/A exons add_range N/A gene chrom N/A gene strand start end N/A last_end end N/A N/A N/A N/A self regions append coding N/A N/A N/A N/A self regions append utr_5 N/A N/A N/A N/A self regions append utr_3 N/A N/A N/A N/A self regions append exons N/A N/A N/A N/A self regions append introns N/A N/A N/A N/A self regions append promoters N/A N/A N/A self counts N/A coding 0 N/A N/A N/A self counts N/A coding-rev 0 N/A N/A N/A self counts N/A other-exon 0 N/A N/A N/A self counts N/A utr-5 0 N/A N/A N/A self counts N/A utr-3 0 N/A N/A N/A self counts N/A utr-5-rev 0 N/A N/A N/A self counts N/A utr-3-rev 0 N/A N/A N/A self counts N/A intron 0 N/A N/A N/A self counts N/A promoter 0 N/A N/A N/A self counts N/A other-exon-rev 0 N/A N/A N/A self counts N/A intron-rev 0 N/A N/A N/A self counts N/A promoter-rev 0 N/A N/A N/A self counts N/A junction 0 N/A N/A N/A self counts N/A intergenic 0 N/A N/A N/A self counts N/A mitochondrial 0 N/A add_read N/A N/A self read chrom N/A N/A N/A N/A read is_unmapped N/A N/A N/A N/A N/A self only_first_fragment N/A read is_paired N/A N/A read is_read1 N/A N/A N/A tag None N/A is_rev False N/A strand N/A N/A read is_reverse - + N/A N/A chrom chrM N/A N/A tag mitochondrial N/A N/A tag N/A N/A N/A op length N/A read cigar N/A N/A N/A op 3 N/A N/A tag junction N/A N/A N/A tag N/A N/A region N/A self regions N/A N/A N/A tag is_rev N/A N/A region get_tag chrom strand N/A read pos N/A tag N/A N/A N/A N/A tag N/A N/A tag intergenic N/A tag N/A N/A is_rev N/A N/A N/A N/A self counts N/A N/A %s-rev tag 1 N/A N/A N/A N/A self counts N/A tag 1 N/A tag N/A tag_region N/A N/A self chrom start end strand N/A N/A N/A tag None N/A is_rev False N/A N/A N/A chrom chrM N/A chrom M N/A N/A tag mitochondrial N/A N/A tag N/A N/A region N/A self regions N/A N/A N/A tag is_rev N/A N/A region get_tag chrom strand start N/A is_rev N/A N/A tag N/A %s-rev tag N/A N/A start end N/A N/A N/A endtag is_rev N/A N/A region get_tag chrom strand end N/A is_rev N/A N/A endtag N/A %s-rev endtag N/A N/A tag endtag N/A endtag tag N/A N/A tag N/A %s/%s N/A tag endtag N/A N/A tag N/A N/A tag intergenic N/A N/A