[EMBOSS] transeq and ambiguous codons

[Peter]

On Thu, Jul 9, 2009 at 10:21 AM, Peter<biopython at maubp.freeserve.co.uk> wrote:
> On Thu, Jul 9, 2009 at 10:16 AM, Peter Rice<pmr at ebi.ac.uk> wrote:
>>
>> Peter C. wrote:
>>
>>> Thanks Scott (& Thomas) for pointing out the embossversion program.
>>>
>>> I would still question why the EMBOSS tools don't also support the
>>> Unix convention of a version switch. Hypothetically, aren't some
>>> (many?) of the tools standalone and couldn't they be installed
>>> individually (e.g. as part of someone else's software bundle)? i.e.
>>> Can EMBOSS really guarantee that the needle tool and the
>>> embossversion tool are in sync?
>>
>> We could easily add a -version global qualifier ... for the next release.
>>
>> We can guarantee that embossversion and needle are in sync - assuming
>> they are built using the same libraries as that is where the version is
>> recorded. Standalone build are an issue though and it would help debug
>> in a few cases.
>
> That sounds good to me :)
>

Thinking about this again, rather than adding a whole new argument
(-version), why not just include the program version as the first line of
the help output (from -help)? This should also solve the corner case
of standalone builds, and makes it very easy to find the version
(without having to know about the embossversion tool).

Thanks,

Peter C.