Problems with naming samples using Gap4

James Bonfield jkb at mrc-lmb.cam.ac.uk
Wed Jan 29 12:02:44 EST 1997


Rifat wrote:

>	I am using Gap4 and found that when the sample files 
>have following name structure e.g.
>
>97_A7_T7_2801.exp

There's a name limitation of 16 characters. This is something which we need to
address and plan to do so. In the mean time I suggest that you keep your
reading names shorter.

Note that reading names need not be the same as filenames. In your case if the
file is called 97_A7_T7_2801.exp then it is possible to have 97_A7_T7_2801 as
the reading name ("ID   97_A7_T7_2801" at the start of the experiment file).

If you already have a whole bunch of experiment files with identifiers ending
in .exp (try (eg) "grep '^ID' *.exp" to list them) then it's possible to run a
script to strip them out of each file. For instance:

#!bin/sh
mkdir new
for i in $@
do
    echo Processing $i
    sed 's/^ID\(.*\)\.exp/ID\1/' < $i > new/$i
done

Save this as strip_exp. Use "chmod a+xr strip_exp", and then do (eg)
"./strip_exp *.exp" to get a directory named "new" containing modified
experiment files. The above description obviously makes assumptions on your
filenames, the exact nature of the problem, and how you generated the
experiment files to start with so tailoring may be necessary.

Good luck,

	James
-- 
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/



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