Module Expr Str Import alias Import alias Import alias ImportFrom alias FunctionDef arguments args NameParam NameParam NameParam NameParam defaults NameLoad body If NameLoad body Assign NameStore BinOpMod Str TupleLoad NameLoad BinOpAdd NameLoad Num Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad If UnaryOpNot NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str NameLoad Return TupleLoad Call AttributeLoad NameLoad attr NameLoad Str NameLoad NameLoad orelse Assign NameStore BinOpMod Str TupleLoad NameLoad BinOpAdd NameLoad Num Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad BinOpMod Str Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad If UnaryOpNot NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str NameLoad Return TupleLoad Call NameLoad NameLoad Str NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam defaults NameLoad NameLoad body Assign NameStore Call NameLoad NameLoad Assign NameStore ListLoad Assign NameStore ListLoad For NameStore Call AttributeLoad NameLoad attr keyword NameLoad body Assign NameStore Num Assign NameStore Num While CompareLt BinOpAdd NameLoad NameLoad Call NameLoad AttributeLoad NameLoad attr body If CompareLtE Call NameLoad NameLoad NameLoad body Assign TupleStore NameStore NameStore NameStore Call NameLoad NameLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad Expr Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad BinOpAdd NameLoad NameLoad keyword BinOpMod Str TupleLoad NameLoad BinOpAdd NameLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad AugAssignAdd NameStore NameLoad AugAssignAdd NameStore Num For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr For TupleStore NameStore NameStore NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults NameLoad body If NameLoad body Print NameLoad Print NameLoad Print Str Expr Call AttributeLoad NameLoad attr Num decorator_list If CompareEq NameLoad Str body Assign NameStore NameLoad Assign NameStore NameLoad Assign NameStore NameLoad Assign NameStore Num Assign NameStore Num Assign NameStore NameLoad For NameStore SubscriptLoad AttributeLoad NameLoad attr Slice Num body If CompareEq NameLoad Str body Expr Call NameLoad If CompareEq NameLoad Str body Assign NameStore Call NameLoad NameLoad Assign NameStore NameLoad orelse If CompareEq NameLoad Str body Assign NameStore Call NameLoad NameLoad Assign NameStore NameLoad orelse If CompareEq NameLoad Str body Assign NameStore NameLoad orelse If CompareIn NameLoad ListLoad Str Str body Assign NameStore NameLoad orelse If UnaryOpNot NameLoad body If UnaryOpNot Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Expr Call NameLoad BinOpMod Str NameLoad Assign NameStore NameLoad orelse If UnaryOpNot NameLoad body Assign NameStore NameLoad If BoolOpOr UnaryOpNot NameLoad UnaryOpNot NameLoad body Expr Call NameLoad Expr Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad
N/A N/A 
For each read in a FASTQ file, split it into smaller (overlapping) chunks.
Fragments are defined by their length and offset. For example, if the length
is 35 and the offset is 10, sub-reads will be 1->35, 11->45, 21->55, etc... If
the offset and the length are the same, then the fragments will not overlap.

Output is a set of (gzip compressed) FASTQ files
 N/A os N/A sys N/A gzip ngsutils.fastq FASTQ _open_file N/A N/A outbase i gz quiet N/A False N/A N/A gz N/A N/A fn N/A %s.%s.fastq.gz N/A outbase N/A i 1 N/A tmp N/A N/A N/A os path join N/A N/A N/A os path dirname fn N/A .tmp.%s N/A N/A N/A os path basename fn N/A N/A quiet N/A N/A N/A N/A N/A sys stderr write N/A Output file: %s
 fn N/A N/A N/A N/A gzip open tmp w tmp fn N/A N/A fn N/A %s.%s.fastq N/A outbase N/A i 1 N/A tmp N/A N/A N/A os path join N/A N/A N/A os path dirname fn N/A .tmp.%s N/A N/A N/A os path basename fn N/A N/A quiet N/A N/A N/A N/A N/A sys stderr write N/A Output file: %s
 fn N/A N/A N/A open tmp w tmp fn N/A fastq_tile N/A N/A fname outbase length offset gz quiet N/A False False N/A N/A fastq N/A FASTQ fname N/A outs N/A N/A fnames N/A N/A read N/A N/A fastq fetch quiet quiet N/A N/A out_idx 0 N/A pos 0 N/A N/A N/A pos length N/A len N/A read seq N/A N/A N/A N/A len outs out_idx N/A N/A N/A fobj tmp fn N/A _open_file outbase out_idx gz quiet N/A N/A N/A outs append fobj N/A N/A N/A fnames append N/A tmp fn N/A N/A N/A N/A N/A read subseq pos N/A pos length comment N/A #tile:%s,%s N/A pos N/A pos length write N/A outs N/A out_idx N/A pos offset N/A out_idx 1 N/A out outs N/A N/A N/A N/A out close N/A N/A N/A fastq close N/A N/A tmp fname fnames N/A N/A N/A N/A os rename tmp fname N/A usage N/A N/A msg N/A None N/A N/A msg N/A N/A msg N/A __doc__ N/A Usage: fastqutils tile {opts} filename.fastq{.gz} out_template

Options:
  -len val         Length of each fragment (default: 35)
  -offset val      Offset for each fragment (default: 10)

  -gz              gzip compress the output FASTQ files

 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 outtemplate None N/A gz False N/A length 35 N/A offset 10 N/A last None N/A arg N/A N/A sys argv N/A 1 N/A N/A N/A arg -h N/A N/A N/A usage N/A N/A last -len N/A N/A length N/A int arg N/A last None N/A N/A N/A last -offset N/A N/A offset N/A int arg N/A last none N/A N/A N/A arg -gz N/A N/A gz True N/A N/A N/A arg N/A -len -offset N/A N/A last arg N/A N/A N/A fname N/A N/A N/A N/A N/A N/A os path exists arg N/A N/A N/A usage N/A Missing file: %s arg N/A fname arg N/A N/A N/A outtemplate N/A N/A outtemplate arg N/A N/A N/A fname N/A outtemplate N/A N/A N/A usage N/A N/A fastq_tile fname outtemplate length offset gz