FASTA format - No funny characters!!

Ledwith, John John.Ledwith at CADUS.COM
Fri Nov 6 10:32:03 EST 1998


Thank you, François.  But lets say I want to set $/ (the input record
separator) to ">".  (Baba) O'Reilly says that you can set it to a
multi-character string, but "^>", "\n>", even "\s>", isnt cutting it (no
pun intended).

Sure, I can find all instances of /*>/ in a multi-FASTA file and replace
the derelict > with some innocent characters (I may start making it IAN
;-)), but that seems like excess time.  So, can someone let me know a
good way to get around this?  Or, as I asked before...

Don't put random >'s in FASTA headers!!!

Please.

Thanks,
john


John Ledwith, Bioinformatics
Cadus Pharmaceutical Corporation
john.ledwith at cadus.com
www.cadus.com
Voicemail: 914-467-6200 x448
Lab: 914-467-6230


	-----Original Message-----
	From:	pingouin at crystal.u-strasbg.fr
[SMTP:pingouin at crystal.u-strasbg.fr]
	Sent:	Friday, November 06, 1998 9:22 AM
	To:	bio-soft at net.bio.net
	Subject:	Re: FASTA format - No funny characters!!

	In article
<2D3428FD6CDFD111A72800104B2351B7242870 at weebo.cadus.com>,
		John.Ledwith at CADUS.COM ("Ledwith, John") writes:
	> As long as we are talking about it...
	> 
	> I cannot count how many times I have come across a FASTA
header with a
	> ">" in the middle of it.  Can we please not let this happen
anymore?
	> PLEASE?!?!?

		Well, I think that this is used in e-mail adresses and
		sometimes in clone numbering, but, anyway, you just have
		to check ^> and not *>

						François.
	-- 
	François Jeanmougin     | groupe de bioinformatique /
bioinformatics groupe
	tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France




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