IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

Combining chopup and reformat?

Guochun Xie xie at splicer.adfa.oz.au
Fri Oct 27 15:38:41 EST 1995


In article <myersm-2510951643310001 at mysersm-pb.rockefeller.edu>,
Michael Myers <myersm at rockvax.rockefeller.edu> wrote:
>In article <1995Oct24.122656.202 at immunbio.mpg.de>,
>GARTMANN at IMMUNBIO.MPG.DE (Christoph Gartmann) wrote:
>
>>In <DGxDo0.Lu9 at argo.net> mcoyne at argo.net writes:
>>
>>> Can anyone tell me of a way to combine chopup and reformat commands in
>>> GCG?  What I'm looking for is perhaps a way to define a command that
>>> would take as an argument a filename, run this through chopup, and
>>> pass the output to reformat, resulting in a GCG format file.
>>> 
>
>Two questions
>1) I use GCG on unix platform. I'm not proficient w/ unix, but could
>someone knowledgable post how to accomplish the above?
  You can use a shell script to do this. The following is an example:
-----Beginning of chopup_reformat.csh ---------
#!/bin/csh
source /home6/gcg/gcgstartup
gcg
chopup  -default -out=$1 $1
reformat $1
-----End of chopup_reformat.csh ---------
Given a sequence file named myseq.seq, you can use "chopup_reformat.csh
myseq.seq" to chopup and reformat the sequence.

I do not use the above approach because it deals only with one sequence
at a time and every execution of the script involves initializing GCG.

I wrote a Perl script which takes a list of sequence files (one line per
sequence file) and convert them to FASTA format. After that, you can
use the "fromfasta" command in GCG to convert the sequences into GCG
format.

If you are interested, I can e-mail  you my Perl script.
  
>
>2) I did not realize that I could put piping instructions on the GCG
>command line. Could someone provide a couple examples of the proper
>syntax? (eg. using reformat to create "file.seq" then pipe to the map
>program).
>
>Michael Myers
>Laboratory of Genetics
>The Rockefeller University
>212-327-8233  (-7420 fax)
>myersm at rockvax.rockefeller.edu

Guochun Xie
Los Alamos National Lab
xie at lanl.gov
-- 
---------------------------------------------------------------------
| Guochun Xie, Ph.D. 				Tel:   505 665-3197 |
| T-10, MS K710					Fax:   505 665-3024 |
| Los Alamos National Laboratory		email: xie at lanl.gov |



More information about the Info-gcg mailing list

Send comments to us at biosci-help [At] net.bio.net