x-rated acedb

Richard Durbin rd at sanger.ac.uk
Wed Sep 27 05:44:05 EST 2000

I think we should create an error if a non IUPAC letter, non white-space
letter is parsed.  To be specific, we should reject the entire
sequence, and create a parse error message like for lines in standard
objects that do not match the model.

Could anyone who objects to this write before the end of this week,
after which we will make the change here unless there is consensus

Given we do this, Keith will have to replace x by n (e.g. with a perl
script) before parsing into acedb.  I think that is reasonable.

Does anyone else rely on being able to read non IUPAC characters?



> acedb> parse
> // Type in your data in .ace format, then CTRL-D to finish
> DNA toto
> atgc
> axgc
> // 1 objects read with 0 errors
> // 1 Active Objects
> acedb> find dna toto
> // Found 1 objects in this class
> // 1 Active Objects
> acedb> show
> DNA : "toto"
>          atgca-gc
> so x is treated as a place holder
> which is probably what yuo want
> considering that some biologists may use it



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