Dear Tim,
That solved the problem. In the event I needed union's -source option
to capture the contig names and a few finds and replaces to get it
displaying well (e.g. changing 'source' features to 'fasta_record'
features, with the name as a 'label' rather than a 'note' in order to
see them), but the end result was very much what I was after.
Many thanks,
Chris
Tim Carver wrote:
Hi Chris
You need to use something like the EMBOSS application 'union'. Separate them
into individual EMBL files and concatenate them into a single EMBL entry
file (use the -feature option and -sformat embl).
Regards
Tim
On 20/3/08 15:18, "Chris Knight" <[EMAIL PROTECTED]> wrote:
I am having difficulties opening an EMBL file in Artemis:
The file in question contains a single genome divided into several
hundred contigs. These contigs are listed in the file I have as separate
entries, each with a separate sequence (SQ) entry- I'd like to read them
all in (and have them appear as separate contigs), however I can only
persuade Artemis to read the first contig.
The separation between the contigs at present is a line containing only
two forward slashes between the end of the preceding contig's sequence
entry (SQ section) and the beginning of the next contig (ID section).
I've tried manipulating the file with Readseq v 2.1.26, which will
happily output everything to fasta format, which allows me to read all
the contigs into Artemis correctly. However, I then lose the annotation
in the embl file. Readseq will separate out the annotation into a
separate .fff file (by using -unpair=1), however, this file is in gff
format v2 and it doesn't seem to read in as an entry into artemis which
wants gff v3 (or rather the file reads, but appears as an empty entry).
Apologies if I've missed something obvious, but any help much appreciated,
Thanks,
Chris
I'm using Artemis release 10 on a Mac running OSX 10.5.2
--
------------------------------------------------------------------------
Dr Christopher Knight Michael Smith Building
Wellcome Trust RCD Fellow Faculty of Life Sciences
Tel: +44 (0)161 2755378 The University of Manchester
room B.2012 Oxford Road
www.dbkgroup.org/MCISB/people/knight/ Manchester M13 9PT
· . ,,><(((°> UK
------------------------------------------------------------------------
_______________________________________________
Artemis-users mailing list
Artemis-users@sanger.ac.uk
http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
