Module Import alias Import alias ImportFrom alias alias Import alias ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias identifier Assign NameStore Call AttributeLoad NameLoad attr NameLoad FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults body Expr Str Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad Call AttributeLoad AttributeLoad NameLoad attr attr Str Dict attr Str ListLoad Num Num Assign NameStore Dict Str Str Dict Str Str NameLoad Str Dict Str Str Call NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Str Str If UnaryOpNot NameLoad body Assign NameStore ListComp TupleLoad NameLoad SubscriptLoad NameLoad Index Str SubscriptLoad NameLoad Index Str comprehension TupleStore NameStore NameStore Call NameLoad NameLoad Expr Call NameLoad Str AttributeLoad NameLoad attr NameLoad orelse Expr Call AttributeLoad NameLoad attr Str For TupleStore NameStore NameStore Call NameLoad NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad SubscriptLoad NameLoad Index Str keyword AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr keyword NameLoad If NameLoad body Assign NameStore BoolOpOr NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr Str NameLoad Assign NameStore IfExp NameLoad NameLoad NameLoad Assign NameStore Call NameLoad keyword SubscriptLoad AttributeLoad NameLoad attr Index Str keyword NameLoad If NameLoad body Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr decorator_list Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Str Str keyword NameLoad keyword Str Call AttributeLoad NameLoad attr Str Str keyword NameLoad keyword Str Call AttributeLoad NameLoad attr Str Str keyword NameLoad keyword Str Call AttributeLoad NameLoad attr Str Str keyword NameLoad keyword Str AttributeLoad NameLoad attr FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str If AttributeLoad NameLoad attr body Assign NameStore Str Assign NameStore Call NameLoad keyword NameLoad keyword Call NameLoad Str keyword Str keyword Call NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call NameLoad Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call NameLoad NameLoad For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword AttributeLoad NameLoad attr decorator_list
N/A N/A logging N/A click click.termui echo style N/A chanjo chanjo.compat iteritems chanjo.config questionnaire chanjo.store Store chanjo.store.models BASE chanjo.store.txmodels BASE TXBASE N/A logger N/A N/A logging getLogger __name__ init N/A N/A context setup reset automate transcripts N/A N/A N/A Walk user through setting up a new config file. N/A N/A N/A click echo N/A chanjo __banner__ N/A cov_tresholds N/A N/A N/A N/A N/A context obj get sambamba N/A get cov_treshold N/A 10 20 N/A defaults N/A sambamba.cov_treshold database N/A value prompt cov_tresholds sufficient coverage N/A value prompt N/A str N/A N/A context obj N/A database central database path/URI N/A N/A automate N/A N/A questions N/A N/A key N/A value N/A prompt N/A value N/A value N/A N/A key value N/A iteritems defaults N/A N/A init_pipeline chanjo N/A context obj questions N/A N/A N/A N/A logger info setting default config values N/A N/A key value N/A iteritems defaults N/A N/A N/A N/A N/A context obj set key N/A value N/A value scope N/A N/A context obj user_data N/A N/A N/A N/A context obj save default_flow_style False N/A setup N/A N/A only_tx N/A transcripts N/A N/A N/A context obj get transcripts False N/A base N/A only_tx TXBASE BASE N/A chanjo_db N/A Store uri N/A N/A context obj N/A database base base N/A reset N/A N/A N/A N/A chanjo_db tear_down N/A N/A N/A chanjo_db set_up N/A N/A N/A click command N/A N/A click option -s --setup is_flag True help setup database tables N/A N/A click option -r --reset is_flag True help reset an existing database N/A N/A click option -a --automate is_flag True help run non-interactively N/A N/A click option -t --transcripts is_flag True help focus only on transcripts on the database level N/A click pass_context init_pipeline N/A N/A program config questions N/A N/A N/A Initializes a config object by interactively asking questions. N/A N/A config user_data N/A N/A message {program} {note}	The existing {file} will be updated N/A segments N/A dict program program note N/A style existing fg yellow file N/A style N/A N/A N/A config config_path basename fg white N/A N/A echo N/A N/A message format segments N/A user_defaults N/A questionnaire questions N/A N/A dot_key value N/A N/A user_defaults items N/A N/A N/A N/A config set dot_key value scope N/A config user_data N/A