[AMOS-help] tarchives2amos script

[David W. <da...@in...>]

Hello

  I have a question about AMOS specifically pertaining to the  
tarchives2amos script. I'm having a problem converting fasta.seq  
files to the .afg format. The problem is that the script seems to  
require a .xml file and I see from the help forum that this is a bug:

Hello everybody,

I just updated Amos from version 2.0.2 to 2.0.4 and the conversion  
utility "tarchive2amos" now requires the presence of the .xml files  
(which was not the case in version 2.0.2).
However, the help message produced by 'tarchive2amos -h' suggests  
that the '.xml' files are not mandatory:

"tarchive2amos -o <prefix> [options] fasta1 ... fastan

<prefix> - prefix for the output files

fasta1 ... fastan - list of files to be converted.
The program assumes that for each file called <file>.seq there
is a <file>.qual and a <file>.xml. (alternatively the files may
be called fasta.<file>, qual.<file> and xml.<file>).
If no .xml file is present the program will only produce a set of
RED (read) records."


Do you know how to get around the bug or is there an update to fix  
the bug. Thanks

David

David Walsh
Postdoctoral fellow
Steven Hallam Laboratory
University of British Columbia
Department of Microbiology & Immunology
Life Sciences Centre
2554-2350 Health Sciences Mall
Vancouver, BC Canada V6T 1Z3
T: 604-827-4216
F: 604-822-6041


da...@in...