Module Import alias Import alias ImportFrom alias ImportFrom alias identifier ImportFrom 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 defaults body Expr Str 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 TryExcept body If NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad With Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr keyword Str NameStore body For NameStore NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad NameLoad attr orelse Expr Call NameLoad NameLoad NameLoad handlers ExceptHandler type NameLoad body Expr Call AttributeLoad NameLoad attr Str decorator_list Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Str Str keyword NameLoad keyword Str Call AttributeLoad NameLoad attr Str keyword NameLoad keyword Call AttributeLoad NameLoad attr keyword Str keyword Str keyword NameLoad AttributeLoad NameLoad attr FunctionDef arguments args NameParam NameParam NameParam defaults Num body Expr Str Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad For TupleStore NameStore NameStore Call NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad If CompareEq BinOpMod NameLoad NameLoad Num body Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str NameLoad Expr Call AttributeLoad NameLoad attr decorator_list
N/A N/A logging N/A click sqlalchemy.exc IntegrityError chanjo.load link link_mod chanjo load chanjo.parse bed chanjo.store Store chanjo.utils validate_stdin chanjo.store.models BASE chanjo.store.txmodels BASE TXBASE N/A logger N/A N/A logging getLogger __name__ link N/A N/A context transcripts bed_stream N/A N/A N/A Link related genomic elements. 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 N/A N/A only_tx N/A N/A result N/A N/A load link_transcripts bed_stream N/A N/A N/A click progressbar N/A result models length N/A result count label adding transcripts bar N/A N/A tx_model bar N/A N/A N/A N/A N/A chanjo_db session add tx_model N/A N/A N/A chanjo_db save N/A N/A N/A link_elements chanjo_db bed_stream N/A N/A N/A IntegrityError N/A N/A N/A N/A click echo elements already linked, use 'chanjo db setup --reset' to re-build N/A N/A N/A click command N/A N/A click option -t --transcripts is_flag True help focus only on transcripts on the database level N/A N/A click argument bed_stream callback validate_stdin type N/A N/A click File encoding utf-8 default - required False N/A click pass_context link_elements N/A N/A chanjo_db bed_iterable batch_size N/A 10000 N/A N/A Load Sambamba BED output from a stream. N/A rows N/A N/A bed chanjo bed_iterable N/A stats N/A N/A link_mod rows N/A chanjo_db session rows N/A N/A index stat N/A enumerate stats N/A N/A N/A N/A chanjo_db add stat N/A N/A N/A index batch_size 0 N/A N/A N/A N/A chanjo_db save N/A N/A N/A logger debug processed %s exons... index N/A N/A N/A chanjo_db save N/A