[emboss-dev] USA syntax and `%' character in sequence file names

[ajb at ebi.ac.uk]

Hi Nicolas,

What it does, given a USA like:

    foo%10

is to seek 10 bytes into file foo and try to start
reading a sequence from there. It does not, however, currently check that
what appears after the '%' is a valid number. I believe invalid numbers
are equivalent to an offset of 0.

I suspect it might have been intended as a useful debugging tool for
the programmer rather than as something for the biologist.
If we leave it as an option we ought to mention it the documentation
in some form though.

ATB

Alan


>
> Hi,
>
> We recently had a problem with a user that tried to use filenames that
> contains `%' characters on our UNIX servers ... It does not seems to
> work as expected, EMBOSS applications truncate the file name to be
> used.
>
> njoly at lanfeust [tmp/geecee]> rm -f foo%bar.data && touch foo%bar.data
> njoly at lanfeust [tmp/geecee]> seqret -sequence=foo%bar.data -auto -stdout
> Error: failed to open filename 'foo'
> Error: Unable to read sequence 'foo%bar.data'
> Died: seqret terminated: Bad value for '-sequence' with -auto defined
>
> Removing the `%' character make this dummy test work as expected.
>
> njoly at lanfeust [tmp/geecee]> rm -f foobar.data && touch foobar.data
> njoly at lanfeust [tmp/geecee]> seqret -sequence=foobar.data -auto -stdout
> Error: Unable to read sequence 'foobar.data'
> Died: seqret terminated: Bad value for '-sequence' with -auto defined
>
> I checked the USA format documentation but did not find any clue. Do
> the `%' character has a special meaning in the USA syntax ?
>
> Thanks.
>
> --
> Nicolas Joly
>
> Biological Software and Databanks.
> Institut Pasteur, Paris.
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