Module Expr Str Import alias identifier Import alias Import alias Import alias identifier ImportFrom alias ImportFrom alias alias alias alias alias alias alias ImportFrom alias alias ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults NameLoad Num body Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr ListLoad Assign NameStore Call NameLoad NameLoad For NameStore NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr ListLoad Call NameLoad SubscriptLoad NameLoad Index Num Call NameLoad SubscriptLoad NameLoad Index Num Expr Call AttributeLoad NameLoad attr Assign TupleStore AttributeStore NameLoad attr AttributeStore NameLoad attr Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad Call NameLoad AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr BoolOpOr NameLoad Str Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return Call NameLoad Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args NameParam NameParam NameParam defaults Num body Assign NameStore Call NameLoad NameLoad For NameStore Call NameLoad NameLoad BinOpAdd NameLoad NameLoad NameLoad body If CompareIn NameLoad AttributeLoad NameLoad attr body Continue Expr Call AttributeLoad AttributeLoad NameLoad attr attr ListLoad NameLoad Num Expr Call AttributeLoad AttributeLoad NameLoad attr attr Assign TupleStore AttributeStore NameLoad attr AttributeStore NameLoad attr Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign AttributeStore NameLoad attr ListComp IfExp CompareGt NameLoad NameLoad ListLoad NameLoad Num ListLoad NameLoad NameLoad comprehension TupleStore NameStore NameStore AttributeLoad NameLoad attr Assign TupleStore AttributeStore NameLoad attr AttributeStore NameLoad attr Call NameLoad AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr keyword Num Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr keyword NameLoad keyword Num Expr Call AttributeLoad NameLoad attr Num AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults Num TupleLoad Str Str body Assign TupleStore NameStore NameStore NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Num Assign NameStore AttributeLoad NameLoad attr For NameStore NameLoad body If CompareEq Call AttributeLoad NameLoad attr Str body Continue Assign TupleStore NameStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr If CompareNotEq NameLoad NameLoad body Continue Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad keyword NameLoad keyword NameLoad orelse Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad keyword NameLoad keyword NameLoad AugAssignAdd NameStore Num Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults Str Num Num body Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad BinOpAdd NameLoad NameLoad NameLoad Assign NameStore ListComp SubscriptLoad NameLoad Index NameLoad comprehension NameStore NameLoad For NameStore AttributeLoad NameLoad attr body If CompareLtELtE NameLoad SubscriptLoad NameLoad Index Num NameLoad body Assign SubscriptStore NameLoad Index Num Num Assign TupleStore AttributeStore NameLoad attr AttributeStore NameLoad attr Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword Num Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword NameLoad keyword Num keyword NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults Str body For NameStore NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr TupleLoad NameLoad NameLoad TupleLoad Num AttributeLoad NameLoad attr Str keyword NameLoad keyword Num decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults NameLoad NameLoad NameLoad Num Str NameLoad NameLoad Num NameLoad Dict TupleLoad Str Str body Assign TupleStore NameStore NameStore NameStore NameStore NameLoad Assign NameStore Num Expr Call AttributeLoad NameLoad attr Call NameLoad TupleLoad BinOpSub NameLoad NameLoad BinOpSub NameLoad NameLoad BinOpAdd NameLoad BinOpMult Num NameLoad BinOpAdd NameLoad BinOpMult Num NameLoad keyword Num keyword NameLoad keyword Str keyword Num Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr NameLoad BinOpAdd NameLoad Str If NameLoad body Assign NameStore ListComp NameLoad comprehension NameStore NameLoad CompareIn SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num NameLoad Expr Call AttributeLoad NameLoad attr keyword Lambda arguments args NameParam defaults Call AttributeLoad NameLoad attr SubscriptLoad Call AttributeLoad NameLoad attr Str Index Num Assign NameStore Call NameLoad NameLoad Assign NameStore BinOpDiv NameLoad NameLoad Assign NameStore BinOpAdd NameLoad NameLoad If CompareIs NameLoad NameLoad body Assign NameStore AttributeLoad Call NameLoad Str Str NameLoad attr orelse Assign NameStore BinOpMult ListLoad NameLoad NameLoad If CompareEq NameLoad Str body Assign NameStore Call AttributeLoad NameLoad attr ListLoad NameLoad BinOpAdd NameLoad NameLoad NameLoad Num Expr Call NameLoad NameLoad ListLoad Str Assign NameStore BinOpAdd NameLoad Num orelse If CompareEq NameLoad Str body Assign NameStore Call AttributeLoad NameLoad attr ListLoad NameLoad BinOpSub NameLoad NameLoad NameLoad Num Expr Call NameLoad NameLoad ListLoad Str Assign NameStore BinOpSub NameLoad Num Assign TupleStore NameStore NameStore NameLoad If NameLoad body Assign NameStore CompareLt NameLoad Num Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad keyword NameLoad If NameLoad body Expr Call AttributeLoad NameLoad attr BinOpAdd NameLoad BinOpDiv NameLoad Num NameLoad NameLoad keyword Str keyword Str keyword Str keyword Num Assign NameStore ListLoad For TupleStore NameStore NameStore NameStore Call NameLoad NameLoad NameLoad NameLoad body AugAssignSub NameStore NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr ListLoad NameLoad NameLoad NameLoad BinOpMult NameLoad Num Assign NameStore Call NameLoad NameLoad NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr keyword NameLoad If NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad If NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad Str attr TupleLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword NameLoad If NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr BinOpSub NameLoad Num BinOpAdd NameLoad BinOpDiv NameLoad Num NameLoad keyword Str keyword Str Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr NameLoad decorator_list decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore IfExp NameLoad NameLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad NameLoad attr BinOpAdd NameLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr ListLoad decorator_list FunctionDef arguments args defaults body Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Str keyword Str Assign TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr If CompareNotEq Call NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr UnaryOpNot Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore NameStore NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr If NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Str Assign NameStore Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr Num TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr ListLoad Num Num Num Num Assign NameStore TupleLoad Num Num Num Num Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad TupleLoad Num NameLoad NameLoad keyword NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr Num Num Expr Call AttributeLoad NameLoad attr Num Num Expr Call AttributeLoad NameLoad attr Assign NameStore BinOpAdd BinOpAdd NameLoad Str AttributeLoad NameLoad attr Expr Call NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword NameLoad decorator_list If CompareEq NameLoad Str body Expr Call NameLoad
N/A N/A 
%prog chrC01 chr.sizes data

Read coverage histogram, similar to wiggle plot. Data contains all the track
data in the form of tab-delimited (x, y) lists.
 N/A os.path op N/A sys N/A logging N/A numpy np jcvi.formats.sizes Sizes jcvi.graphics.base plt savefig Rectangle mb_formatter mb_float_formatter adjust_spines get_map jcvi.apps.base OptionParser glob XYtrack N/A object N/A __init__ N/A N/A self ax datafile color ymax N/A None 40 N/A N/A N/A self ax ax N/A N/A self xy N/A N/A fp N/A open datafile N/A row fp N/A N/A atoms N/A N/A row split N/A N/A N/A N/A self xy append N/A N/A int N/A atoms N/A 0 N/A float N/A atoms N/A 1 N/A N/A N/A fp close N/A N/A N/A self x N/A self y N/A zip N/A self xy N/A N/A N/A logging debug N/A N/A File `{0}` imported (records={1}). format datafile N/A len N/A self x N/A N/A self color N/A color k N/A N/A self ymax ymax N/A mapping N/A N/A self N/A N/A N/A N/A dict N/A zip N/A self x N/A self y N/A property interpolate N/A N/A self maxsize unit N/A 10000 N/A N/A maxsize N/A int maxsize N/A pos N/A range unit N/A maxsize unit unit N/A N/A N/A pos N/A self x N/A N/A N/A N/A N/A N/A self xy append N/A pos 0 N/A N/A N/A N/A self xy sort N/A N/A N/A self x N/A self y N/A zip N/A self xy N/A N/A N/A logging debug N/A N/A After interpolate: {0} format N/A len N/A self x N/A cap N/A N/A self ymax N/A N/A N/A N/A self xy N/A N/A N/A b ymax N/A a 0 N/A a b N/A N/A a b N/A self xy N/A N/A N/A self x N/A self y N/A zip N/A self xy N/A draw N/A N/A self N/A N/A N/A ax N/A self ax N/A color N/A self color N/A N/A N/A ax plot N/A self x N/A self y lw 0 N/A N/A N/A ax fill_between N/A self x N/A self y color color lw 0 N/A N/A N/A ax set_ylim 0 N/A self ymax N/A N/A N/A ax set_axis_off N/A import_hlfile N/A N/A self hlfile chr unit diverge N/A 10000 N/A r g N/A N/A N/A rr gg diverge N/A fp N/A open hlfile N/A imported 0 N/A mapping N/A self mapping N/A row fp N/A N/A N/A N/A N/A row strip N/A N/A N/A N/A seqid start end tag N/A N/A row split N/A N/A seqid chr N/A N/A N/A start N/A int start N/A end N/A int end N/A N/A tag double N/A N/A N/A N/A self highlight mapping start end color rr unit unit N/A N/A N/A N/A self highlight mapping start end color gg unit unit N/A imported 1 N/A N/A N/A logging debug N/A N/A Imported {0} regions from file `{1}`. format imported hlfile N/A highlight N/A N/A self mapping start end color unit zorder N/A r 10000 10 N/A N/A ax N/A self ax N/A x N/A range start N/A end unit unit N/A y N/A N/A mapping N/A z N/A z x N/A a N/A self xy N/A N/A N/A start N/A a N/A 0 end N/A N/A N/A a N/A 1 0 N/A N/A N/A self x N/A self y N/A zip N/A self xy N/A N/A N/A ax plot x y lw 0 N/A N/A N/A ax fill_between x y color color lw 0 zorder zorder N/A vlines N/A N/A self xs color N/A m N/A N/A x xs N/A N/A N/A N/A N/A self ax plot N/A x x N/A 0 N/A self ymax - color color lw 2 N/A N/A Coverage N/A object N/A __init__ N/A N/A self fig root canvas chr xlim datadir order hlsuffix palette cap gauge plot_label plot_chr_label gauge_step vlines labels_dict diverge N/A None None None 50 bottom True True 5000000 None N/A N/A r g N/A N/A N/A x y w h canvas N/A p 0.01 N/A N/A N/A root add_patch N/A Rectangle N/A N/A x p N/A y p N/A w N/A 2 p N/A h N/A 2 p lw 1 fill False ec darkslategray zorder 10 N/A datafiles N/A glob N/A N/A op join datadir N/A chr * N/A order N/A N/A datafiles N/A z N/A z datafiles N/A N/A N/A N/A z split . N/A 1 order N/A N/A N/A datafiles sort key N/A N/A N/A x N/A N/A N/A order index N/A N/A N/A x split . N/A 1 N/A ntracks N/A len datafiles N/A yinterval N/A h ntracks N/A yy N/A y h N/A N/A palette None N/A N/A set2 N/A N/A get_map Set2 qualitative ntracks mpl_colors N/A N/A set2 N/A N/A palette ntracks N/A N/A gauge top N/A N/A gauge_ax N/A N/A fig add_axes N/A x N/A yy p w 0.0001 N/A N/A adjust_spines gauge_ax N/A top N/A tpos N/A yy 0.07 N/A N/A N/A gauge bottom N/A N/A gauge_ax N/A N/A fig add_axes N/A x N/A y p w 0.0001 N/A N/A adjust_spines gauge_ax N/A bottom N/A tpos N/A y 0.07 N/A N/A start end xlim N/A gauge N/A N/A fs N/A gauge_step 1000000 N/A N/A setup_gauge_ax gauge_ax start end gauge_step float_formatter fs N/A plot_chr_label N/A N/A N/A N/A root text N/A x N/A w 2 tpos chr ha center va center color darkslategray size 16 N/A yys N/A N/A N/A label datafile c N/A zip order datafiles set2 N/A N/A yy yinterval N/A N/A N/A yys append yy N/A ax N/A N/A fig add_axes N/A x yy w N/A yinterval 0.9 N/A xy N/A XYtrack ax datafile color c N/A N/A N/A xy interpolate end N/A N/A N/A xy cap ymax cap N/A vlines N/A N/A N/A N/A xy vlines vlines N/A hlsuffix N/A N/A hlfile N/A N/A op join datadir N/A N/A . join N/A label hlsuffix N/A N/A N/A xy import_hlfile hlfile chr diverge diverge N/A plot_label N/A N/A label N/A N/A labels_dict get label N/A N/A label capitalize N/A label N/A N/A \textit{{{0}}} format label N/A N/A N/A root text N/A x 0.015 N/A yy N/A yinterval 2 label ha right va center N/A N/A N/A xy draw N/A N/A N/A ax set_xlim xlim N/A N/A self yys yys N/A N/A setup_gauge_ax N/A N/A gauge_ax start end gauge_step float_formatter N/A False N/A N/A N/A N/A gauge_ax set_xlim start end N/A formatter N/A float_formatter mb_float_formatter mb_formatter N/A N/A N/A N/A gauge_ax xaxis set_major_formatter formatter N/A N/A N/A N/A gauge_ax xaxis set_ticks N/A N/A np arange N/A start gauge_step end gauge_step N/A N/A N/A N/A gauge_ax yaxis set_ticks N/A N/A main N/A N/A N/A N/A N/A p N/A OptionParser __doc__ N/A N/A N/A p add_option --order help The order to plot the tracks, comma-separated N/A N/A opts args iopts N/A N/A p set_image_options N/A N/A N/A len args 3 N/A N/A N/A N/A sys exit N/A N/A N/A p print_help N/A N/A chr sizes datadir args N/A order N/A opts order N/A hlsuffix N/A opts hlsuffix N/A order N/A N/A order N/A N/A order split , N/A sizes N/A Sizes sizes N/A fig N/A N/A plt figure 1 N/A N/A iopts w N/A iopts h N/A root N/A N/A fig add_axes N/A 0 0 1 1 N/A canvas N/A 0.12 0.35 0.8 0.35 N/A chr_size N/A N/A sizes get_size chr N/A N/A Coverage fig root canvas chr N/A 0 chr_size datadir order order hlsuffix hlsuffix N/A N/A N/A root set_xlim 0 1 N/A N/A N/A root set_ylim 0 1 N/A N/A N/A root set_axis_off N/A image_name N/A N/A chr . N/A iopts format N/A N/A savefig image_name dpi N/A iopts dpi iopts iopts N/A N/A N/A __name__ __main__ N/A N/A N/A main