File of filenames in pregap

James Bonfield jkb at mrc-lmb.cam.ac.uk
Wed Dec 11 13:06:15 EST 1996

Jan Gielen wrote:

>When I start pregap, the first thing you need
>is a file of filenames. When I want to do interactive
>quality clipping, the program gives me always the last file
>from the file of filenames.It's like the files 
>have all the same names and the program overwrights them 
>every time, although they all have different names.

This could be due to having the same sample name in each of your files. As
I've now seen several cases like this I added a bit to the pregap manual
(http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap_6.html). To summarise:

	It is sometimes useful to determine the experiment file names
	and reading names from an ABI filename rather than the sample
	named contained within it. If this is your usual form of
	working then modify the abi_SCF_com, abi_Exp_com and
	abi_Ent_com variables. An example would be to add the
	following to your `.pregaprc' file.

	abi_SCF_com='echo "${file}.scf"'
	abi_Exp_com='echo "${file}.exp"'
	abi_Ent_com='echo "${file}" | sed "s/ /_/g"'

This _may_ fix things for you.


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