Module Expr Str Import alias Import alias ImportFrom alias Assign NameStore Dict Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad For NameStore Call AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad Return Call AttributeLoad Str attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults AttributeLoad NameLoad attr NameLoad body For NameStore Call AttributeLoad NameLoad attr keyword NameLoad body If CompareIn SubscriptLoad AttributeLoad NameLoad attr Index Num Str body Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Slice Num Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Slice Num orelse Assign NameStore SubscriptLoad NameLoad Slice Num Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Slice Num Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad AttributeLoad NameLoad attr Call NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args defaults body Print NameLoad Print Str Expr Call AttributeLoad NameLoad attr Num decorator_list If CompareEq NameLoad Str body Assign NameStore NameLoad For NameStore SubscriptLoad AttributeLoad NameLoad attr Slice Num body If Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Assign NameStore NameLoad If UnaryOpNot NameLoad body Expr Call NameLoad Assign NameStore Call NameLoad NameLoad Expr Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr
N/A N/A 
Convert color-space FASTQ file to encoded color-space.

This is required for some tools that don't natively support color-space
files, such as BWA. For these tools, the color-space 01234 must be converted
into an encoded ACGTN.

0 -> A
1 -> C
2 -> G
3 -> T
4,5,6,. -> N
 N/A os N/A sys ngsutils.fastq FASTQ N/A _encoding N/A 0 1 2 3 4 5 6 . A C G T N N N N encoded_seq N/A N/A seq N/A N/A N/A ret N/A N/A s N/A N/A seq upper N/A N/A N/A N/A ret append N/A _encoding N/A s N/A N/A N/A join ret N/A fastq_csencode N/A N/A fastq out quiet N/A N/A sys stdout False N/A N/A read N/A N/A fastq fetch quiet quiet N/A N/A N/A N/A N/A read seq N/A 0 ATCG N/A N/A seq N/A N/A read seq N/A 2 N/A qual N/A N/A read qual N/A 1 N/A N/A seq N/A seq N/A 1 N/A qual N/A N/A read qual N/A 1 N/A N/A N/A out write N/A @%s
%s
+
%s
 N/A N/A read name N/A encoded_seq seq qual N/A usage N/A N/A N/A N/A N/A __doc__ N/A Usage: fastqutils csencode filename.fastq{.gz} 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 arg N/A N/A sys argv N/A 1 N/A N/A N/A N/A N/A os path exists arg N/A N/A fname arg N/A N/A fname N/A N/A N/A usage N/A fq N/A FASTQ fname N/A N/A fastq_csencode fq N/A N/A N/A fq close