Module ImportFrom alias Import alias Import alias Import alias Import alias Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore NameLoad FunctionDef arguments args NameParam NameParam NameParam defaults body Global identifier If CompareIs NameLoad NameLoad body Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr orelse Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad BinOpAdd NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr BinOpAdd NameLoad Str Str keyword NameLoad Assign NameStore Call AttributeLoad NameLoad attr BinOpAdd NameLoad Str Str keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Num For TupleStore NameStore NameStore NameStore NameStore NameLoad body Print NameLoad BinOpMod Str TupleLoad NameLoad NameLoad NameLoad NameLoad NameLoad Print NameLoad BinOpMod Str TupleLoad NameLoad NameLoad NameLoad NameLoad AugAssignAdd NameStore Num If CompareIsNot NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign TupleStore NameStore NameStore TupleLoad Str ListLoad Assign NameStore Call AttributeLoad NameLoad attr Str Str NameLoad Assign NameStore Call AttributeLoad NameLoad attr Str Str NameLoad Assign NameStore Call AttributeLoad NameLoad attr While NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Str NameLoad If UnaryOpNot NameLoad body Break Assign TupleStore NameStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr AugAssignAdd NameStore NameLoad Expr Call AttributeLoad NameLoad attr TupleLoad Call NameLoad NameLoad BinOpAdd Call NameLoad NameLoad Call NameLoad NameLoad NameLoad NameLoad AugAssignAdd NameStore NameLoad AugAssignAdd NameStore NameLoad Return TupleLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Num Assign NameStore ListLoad With Call AttributeLoad NameLoad attr NameLoad keyword NameLoad NameStore body For NameStore NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Str TryExcept body Assign TupleStore NameStore NameStore NameStore Call AttributeLoad NameLoad attr Str Num handlers ExceptHandler type NameLoad body Assert NameLoad BinOpMod Str NameLoad Assign NameStore Call AttributeLoad NameLoad attr Str Str Assign TupleStore NameStore NameStore Call NameLoad NameLoad Assign TupleStore NameStore NameStore Call NameLoad NameLoad AugAssignAdd NameStore Str AugAssignAdd NameStore Str Assign NameStore BinOpAdd NameLoad NameLoad Assign NameStore BinOpAdd NameLoad ListComp TupleLoad BinOpAdd SubscriptLoad NameLoad Index Num Call NameLoad NameLoad BinOpAdd SubscriptLoad NameLoad Index Num Call NameLoad NameLoad SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num comprehension NameStore NameLoad Expr Call NameLoad NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Global identifier Assign NameStore NameLoad Assign NameStore SubscriptLoad NameLoad Slice Num If BoolOpAnd CompareGt Call NameLoad NameLoad Num CompareEq SubscriptLoad NameLoad Index Num Str body Assign NameStore SubscriptLoad NameLoad Index Num Print AttributeLoad NameLoad attr BinOpMod Str NameLoad Assign NameStore SubscriptLoad NameLoad Slice Num Assign NameStore Num For NameStore NameLoad body TryExcept body Expr Call NameLoad NameLoad handlers ExceptHandler type NameLoad name NameStore body Print AttributeLoad NameLoad attr BinOpMod Str TupleLoad NameLoad NameLoad AugAssignAdd NameStore Num If CompareGt NameLoad Num body Print AttributeLoad NameLoad attr BinOpMod Str TupleLoad NameLoad Call NameLoad NameLoad decorator_list If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr Call NameLoad AttributeLoad NameLoad attr
N/A __future__ with_statement N/A sys N/A os N/A re N/A codecs N/A INPUT_ENCODING UTF-8 N/A OUTPUT_ENCODING UTF-8 N/A ENTITY_TYPE Disease N/A ATTR_TYPE Category N/A FILE_PREFIX PMID- N/A output_directory None output N/A N/A docid text anns N/A N/A N/A output_directory N/A N/A output_directory None N/A N/A txtout N/A sys stdout N/A soout N/A sys stdout N/A N/A outfn N/A N/A N/A os path join output_directory N/A FILE_PREFIX docid N/A txtout N/A N/A codecs open N/A outfn .txt wt encoding OUTPUT_ENCODING N/A soout N/A N/A codecs open N/A outfn .ann wt encoding OUTPUT_ENCODING N/A N/A N/A txtout write text N/A idseq 1 N/A N/A start end type_ text anns N/A N/A soout N/A T%d	%s %d %d	%s N/A idseq ENTITY_TYPE start end text N/A soout N/A A%d	%s T%d %s N/A idseq ATTR_TYPE idseq type_ N/A idseq 1 N/A N/A output_directory None N/A N/A N/A N/A txtout close N/A N/A N/A soout close N/A parse N/A N/A s N/A N/A N/A N/A text anns N/A N/A N/A s N/A N/A re sub (<category[^<>]*>)( +) \2\1 s N/A s N/A N/A re sub ( +)(<\/category>) \2\1 s N/A rest N/A N/A s strip N/A True N/A N/A m N/A N/A re match ^(.*?)<category="([^"]+)">(.*?)</category>(.*)$ rest N/A N/A m N/A N/A N/A N/A pre type_ tagged rest N/A N/A m groups N/A text pre N/A N/A N/A anns append N/A N/A len text N/A N/A len text N/A len tagged type_ tagged N/A text tagged N/A text rest N/A N/A text anns N/A process N/A N/A fn N/A N/A N/A docnum 1 N/A sentences N/A N/A N/A N/A codecs open fn encoding INPUT_ENCODING f N/A N/A l f N/A N/A l N/A N/A l strip N/A N/A N/A N/A PMID title body N/A N/A l split 2 N/A N/A N/A ValueError N/A N/A False N/A Expected three TAB-separated fields, got '%s' l N/A body N/A N/A body replace N/A N/A t_text t_anns N/A parse title N/A N/A b_text b_anns N/A parse body N/A t_text N/A b_text N/A text N/A t_text b_text N/A anns N/A t_anns N/A N/A N/A N/A a N/A 0 N/A len t_text N/A N/A a N/A 1 N/A len t_text N/A a N/A 2 N/A a N/A 3 N/A a b_anns N/A N/A output PMID text anns N/A main N/A N/A argv N/A N/A N/A output_directory N/A output_directory None N/A filenames N/A argv N/A 1 N/A N/A N/A N/A len argv 2 N/A N/A argv N/A 1 -o N/A N/A output_directory N/A argv N/A 2 N/A N/A sys stderr N/A Writing output to %s output_directory N/A filenames N/A argv N/A 3 N/A fail_count 0 N/A fn filenames N/A N/A N/A N/A N/A process fn N/A N/A N/A Exception N/A e N/A N/A N/A sys stderr N/A Error processing %s: %s N/A fn e N/A fail_count 1 N/A N/A fail_count 0 N/A N/A N/A sys stderr N/A 
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# WARNING: error in processing %d/%d files, output is incomplete!
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 N/A fail_count N/A len filenames N/A N/A N/A __name__ __main__ N/A N/A N/A N/A sys exit N/A main N/A sys argv