[EMBOSS] Problems converting sequences with seqret

simon andrews (BI) simon.andrews at bbsrc.ac.uk
Mon Jan 26 16:03:44 UTC 2004

> -----Original Message-----
> From: James Sinnott [mailto:sinnottj at cs.man.ac.uk] 
> Sent: 26 January 2004 15:25
> To: emboss at embnet.org
> Subject: [EMBOSS] Problems converting sequences with seqret
> However, I've found a problem in that seqret seems to output 
> some sequence formats that it cannot subsequently re-read!  
> several of the msf and all of the nexus files were found 
> to be unreadable by seqret when trying to re-convert them.

There looks to be a bug in seqret.  I can't reproduce this 
with msf files (may just be the data I was using), but 
certainly there's something wrong with the nexus parser.

If you use the dna.msf file included with EMBOSS as a test 

$ uname -sr
Linux 2.4.22-1.2149.nptlsmp
$ embossversion
Writes the current EMBOSS version number
$ seqret /usr/local/share/EMBOSS/test/data/dna.msf nexus::nexus.txt
Reads and writes (returns) sequences
$ seqret nexus::nexus.txt fasta::stdout
Reads and writes (returns) sequences
Segmentation fault

Running a debug on the second process doesn't show much.  The 
matrix seems to be read OK, but then it segfaults.  An strace 
on the process doesn't show any system calls going awry so 
I'm not sure what's going wrong.

Certainly something to look at...


Simon Andrews PhD
Bioinformatics Dept
The Babraham Institute

simon.andrews at bbsrc.ac.uk
+44 (0)1223 496463

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