[EMBOSS] Problems converting sequences with seqret
James Sinnott
sinnottj at cs.man.ac.uk
Mon Jan 26 15:24:33 UTC 2004
Hi,
I'm building an application that should allow the user to work with a set of
sequences in an arbitrary format (e.g. FastA) regardless of the formats the
sequences may actually be stored in (clustal, nexus, msf, etc.) I need to be
able to convert sequences to and back-from the users' desired format behind
the scenes, and seqret seems to be the most suitable tool for this.
However, I've found a problem in that seqret seems to output some sequence
formats that it cannot subsequently re-read!
As an example, I converted a set of FastaA files into clustal, phylip, msf, &
nexus formats and then tried to re-convert the files back into FastA format.
The clustal & phylip files all worked OK, but several of the msf and all of
the nexus files were found to be unreadable by seqret when trying to
re-convert them.
Am I doing anything wrong? Is this a common issue with seqret?
Any help would be gratefully accepted!
Best regards,
James Sinnott.
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