bug ?

Brian Fristensky frist
Wed Nov 16 12:52:40 EST 1994

> From daemon Wed Nov 16 11:42:47 1994
> Date: Wed, 16 Nov 1994 18:42:32 +0000
> From: blacroix at jetset (Bruno Lacroix)
> To: frist at pssun1.plants.umanitoba.ca
> Subject: bug ?
> Content-Length: 676
> Hi,
> I am currently in the process of testing the xylem package on a Solaris 2
> workstation. I had no real problem compiling and linking the various
> executables, but I ended with what seems to be a bug (or at least a potential
> problem). Indeed, when trying to split Genbank with splitdb, I got incorrect
> .wrp files. I found out that this was a problem with the Genbank files I was
> using, where every line ended with both a newline and a carriage return (those
> files were directly downloaded from NCBI Genbank CDROM). Removing the extra
> carriage return solved the problem.
> Does this remind you of something, and do you think you can fix this in splitdb
> code ?
> Sincerely.
> 	Bruno.
There's nothing to fix. In Unix, lines end with <RETURN>, whereas in DOS they end
with <RETURN><LINEFEED>. If NCBI distributes GenBank formatted for DOS,
it is should be standard procedure to remove <LINEFEED> characters at
the end of lines when copying these files onto a Unix system. If you
don't, any program that is expecting a Unix-style line will have a problem.
Solaris comes with a set of programs called 'dos2unix' and 'unix2dos'.
To convert a DOS file to Unix, type

dos2unix < original_file > new_file

I haven't encountered this problem before because I always obtain GenBank
by FTP. 

Brian Fristensky                | 
Department of Plant Science     |  Life doesn't imitate art,
University of Manitoba          |  it imitates bad television. 
Winnipeg, MB R3T 2N2  CANADA    |  
frist at cc.umanitoba.ca           |  
Office phone:   204-474-6085    |  Woody Allen, HUSBANDS AND WIVES  
FAX:            204-261-5732    |  

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