Pise/EMBOSS 2.3.1

[Peter Rice]

Hi Catherine,

> Main changes were for align types, where I could associate a "pipetype" to
> chain to other programs taking alignment as input. BTW, I found "MSF" and "fasta" for the
> -aformat parameter - are there others?

There are more, but not sequence formats. We should add them to "entrails"
output.

We can easily add more sequence formats. Can you suggest some?

The full list is (from ajax/ajalign.c) :

markx0*, markx1*, markx2*, markx3*, markx10* (from the FASTA package)
multiple
pair*
simple
score
srs, srspair* (for simple parsing in SRS in case the others change)
trace (for debugging only)

Those with '*' are for pairwise alignments only.

> The main problem I had was with string parameters for specifying a path, with ./ default
> value and having corresponding extn parameters.
>
> That's why I had to discard the following programs:
> alignwrap, contacts, seqnr, seqsort, siggen, dichet and scopalign.
>
> A solution could be to have an explicit type and the extension as an attribute:
> 
> path: algpath  [
>   parameter: "Y"
>   prompt: "Location and extension of alignment files for input"
>   default: "./"
>   extn: ".align"
> ]
> 
> What do you think?

The path and extension options  are a terrible 'hack' to avoid having "*"
on the command line for those programs.

This is really just infile with a wild card filename (which works already).

We can make a new ACD type "inwild" which works like infile but with some
small differences. The prompt would be "Input file(s)". The ajAcdGetInwild
function will return an AjPFile. We can add functions to report the
filenames as a string list (the first file is already open, the others are
in a list so it is a little tricky to make the list in an application).

There should be an attribute "inextension:align" (for example) and a
default value of "*". If the user specifies "*.align" the inextension will
be ignored.

Associated qualifiers:

-inextension align
-indirectory /home/user/somewhere (defaults to current directory)

For consistency, we can add the same qualifiers for infile.

With "out" instead of "in" we can sue the same qualifiers for outfile and a
new ACD type "outwild" (outwild can open a new output file, using a new
ajFileNextOut call, but the application needs to give the base name each
time).

All easy to implement.

One problem ... inwild does not work well as a parameter because it has to
be given as "*" on the command line. Same problem for "outwild". I am sure
users can be educated.

The programs that use the path/extension options do not define them as
parameters anyway. Their ACD files need some corrections.

Comments?

regards,

Peter

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723