Module Expr Str Import alias Import alias ImportFrom alias FunctionDef arguments args NameParam NameParam defaults Str body Assign NameStore NameLoad Assign NameStore Str Assign NameStore ListLoad FunctionDef arguments args defaults body If NameLoad body Return BinOpMod Str TupleLoad NameLoad Call NameLoad NameLoad orelse Return BinOpMod Str TupleLoad NameLoad Call NameLoad NameLoad decorator_list For NameStore Call NameLoad NameLoad keyword NameLoad body If CompareEq SubscriptLoad NameLoad Index Num Str body Assign NameStore SubscriptLoad Call AttributeLoad Call AttributeLoad SubscriptLoad NameLoad Slice Num attr attr Str Index Num If CompareIn NameLoad NameLoad body Assign NameStore NameLoad Expr Call AttributeLoad NameLoad attr NameLoad orelse Assign NameStore NameLoad If NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str For NameStore NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str NameLoad decorator_list FunctionDef arguments args NameParam defaults NameLoad body If NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str Expr Call AttributeLoad NameLoad attr Num decorator_list If CompareEq NameLoad Str body Assign NameStore NameLoad Assign NameStore Str For NameStore SubscriptLoad AttributeLoad NameLoad attr Slice Num body If UnaryOpNot NameLoad body If Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Assign NameStore NameLoad orelse Expr Call NameLoad BinOpMod Str NameLoad orelse Assign NameStore NameLoad If UnaryOpNot NameLoad body Expr Call NameLoad Expr Call NameLoad NameLoad NameLoad
N/A N/A 
Strips alternative assemblies from reference FASTA files

This removes all sequences by looking for specific substrings in their name
(defaults to '_')

 N/A sys N/A os eta eta_open_iter strip_fasta N/A N/A fname substr N/A _ N/A N/A good False N/A name N/A rmlist N/A callback N/A N/A N/A N/A N/A good N/A N/A N/A %s (removed %s) N/A name N/A len rmlist N/A N/A N/A %s [x] (removed %s) N/A name N/A len rmlist N/A N/A line N/A eta_open_iter fname callback callback N/A N/A N/A N/A line N/A 0 > N/A N/A name N/A N/A N/A N/A N/A N/A line N/A 1 strip split N/A 0 N/A N/A substr name N/A N/A good False N/A N/A N/A rmlist append name N/A N/A good True N/A good N/A N/A N/A N/A N/A sys stdout write line N/A N/A N/A N/A sys stderr write Removed:
 N/A n rmlist N/A N/A N/A N/A N/A sys stderr write N/A %s
 n N/A usage N/A N/A msg N/A None N/A N/A msg N/A N/A N/A N/A N/A sys stdout write N/A %s
 msg N/A N/A N/A N/A sys stdout write __doc__ N/A N/A N/A N/A sys stdout write Usage: ngsutils strip_fasta filename.fa [string-to-search-for]

 N/A N/A N/A sys exit 1 N/A N/A N/A __name__ __main__ N/A N/A fname None N/A substr _ N/A arg N/A N/A sys argv N/A 1 N/A N/A N/A fname N/A N/A N/A N/A N/A os path exists arg N/A N/A fname arg N/A N/A N/A usage N/A %s missing! arg N/A N/A substr arg N/A N/A fname N/A N/A N/A usage N/A N/A strip_fasta fname substr