[CORRECTION] Re: FASTA format - No funny characters!!

Ledwith, John John.Ledwith at CADUS.COM
Fri Nov 6 15:41:36 EST 1998


Thank you, Roland!  Just you writing it out made my code work.  Really.
Programming is such a funny exercise. :-)

Have a good weekend, all.

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:	Roland Walker [SMTP:walker at ncbi.nlm.nih.gov]
	Sent:	Friday, November 06, 1998 12:00 PM
	To:	bio-soft at net.bio.net
	Subject:	[CORRECTION] Re: FASTA format - No funny
characters!!

	[sorry, typing too fast]

	[John.Ledwith at CADUS.COM writes]
	> Thank you, Fran?ois.  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).

	#!/bin/perl
	$/="\n>";
	while (<>) {
	  chomp;
	  s/\A>?([^\n]*)\n//;
	  tr/\n//d;
	  my $defline=">$1";
	  my $sequence=$_;

	  $defline =~ s/\A([^\cA]{1,80}).*/$1/; # Example: 
	                                        # limit defline to max
80 columns
	                                        # or up to the first
control-A


	  # other transformations left as
	  # an exercise to the reader

	  print "$defline\n$sequence\n";

	}

	-- 

	Roland Walker
	walker at ncbi.nlm.nih.gov
	National Center for Biotechnology Information




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