In article <9109301300.AA05395 at lux.think.com>, jones at Think.COM (Robert Jones) writes:
>> From: wrp at biochsn.acc.Virginia.EDU (William R. Pearson)
> Newsgroups: bionet.software
> Organization: University of Virginia
> One of the things I would very much like to see would be a
> general set of of programs for indexing/extracting sequences from any
> standard database format.
>>>>>>>>>(offer to contribute to the effort deleted)
>> Bill Pearson
>>In the computer graphics field there is a very simple and efficient way of
>handling conversions between the many image formats. The Portable Bitmap
>Toolkit (PBM)provides a single 'central' image format along with a set of small
>unix programs, used as filters, to take TIFF files, for example, into the
>central format and then convert that to, say, an X11 bitmap.
>>>>>>>>> (more description deleted ML)
>>I was thinking about setting up an equivalent for sequence files and
>database extraction could readily fall into this. For someone familiar with
>UNIX it would be straightforward to use and some simple wrapper could be
>written for novices. Would this be of interest ? Is it an appropriate way
>to handle this sort of data ?
>YES IT IS: very much so! In the past year I've gone through "Filetype
Frustration" so many time I started writing my own filters. While GCG
provides some filetype conversion utilities they are incomplete, as they
are geared to conversions to and from GCG format. While I do most of my
stuff with GCG and (now) programs that can read GCG (Malign), there are
times that passing something through GCG format is just another step.
The GCG programs also require a GCG liscense. While there seem to be a
number of other file conversion utilities out there, I don't think there
is an easily extensible system with a consistent interface like PBM.
>There are a number of format conversion tools out there of varying complexity
>and it may be appropriate to adapt one of these rather than start up
>something new - but I do like the PBM approach. I'd be willing to put in a
>share of the work on something like this.
>>Robert Jones jones at think.com
Please do it. PS: It would be nice if the same basic system ran on Unix and
VMS, so that individual "format modules" could be used with either.
Mike Lonetto lonetto at psl.wisc.edu
UW-Madison Dept. of Bacteriology