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Can someone please provide the *exact* specification of MSF format?

Jan T. Kim a1624091 at athena.rrz.uni-koeln.de
Tue Oct 25 14:19:50 EST 1994


Eric L. Cabot (elmo at helix.nih.gov) wrote:
: Hello world!
:   Can someone please supply me with the exact specification
: of the GCG-MSF format. I need it for a program that I am writing.
: More specifically, I would like to have my program produce multiple
: sequence files that can be used by the appropriate GCG programs.
: I sent a similar email query to help at gcg.com a couple of weeks
: ago but go no reply!
: 
: It sure would be nice if there was a utilitity that took one of
: the cleaner formats, oh-say Fasta or PIR/NBRF, and converted to
: MSF -- but there isn't.

You could convert from a PIR multiple sequence file to a GCG
MSF file in a two step procedure:

1. Convert from PIR to plain GCG sequence format using FROMPIR:

    $ frompir myseqs.pir

will create a bunch of files named seqname.gcg extracted from
your PIR file in your current directory.

2. Reformat these GCG sequences into on a MSF file:

    $ reformat /msf

    [... some info on REFORMAT]

    REFORMAT what sequence file(s)? *.gcg
                                    ^^^^^
                                    Enter answer here

After specifying the MSF's filename, REFORMAT creates a MSF file
containing the sequences from the original PIR file (if you didn't
have any previously existing *.gcg file in the working directory).

Writing your own stuff to create GCG formatted sequences is
always messy -- at least, I know someone who once tried and
failed to find any documentation on the checksum algorithm,
so he finally figured it out by guessing.

Greetinx, Jan
--
 +- Jan Kim -- X.400:    S=kim;OU=vax;O=mpiz-koeln;P=mpg;A=d400;C=de -+
 |             Internet: kim at vax.mpiz-koeln.mpg.d400.de               |
 |                                                                    |
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