[EMBOSS] Does seqret have limitations ?

simon andrews (BI) simon.andrews at bbsrc.ac.uk
Tue Dec 16 16:46:39 UTC 2003

-----Original Message-----
From: Barretto,Caroline,LAUSANNE,NRC/BAS [mailto:Caroline.Barretto at rdls.nestle.com] 
Sent: 16 December 2003 16:12
To: emboss at embnet.org
Subject: [EMBOSS] Does seqret have limitations ?

> Dear all,
> Did anybody notice that the seqret program seems to 
> be limited by the number of sequences to convert ? I 
> am trying to convert 1 file containing 23000 genbank 
> sequences into GCG format.
> Do you have a suggestion for that ?

Seqret is not limited by number of files.  I routinely pass the whole of EMBL through seqret and it works fine.  What error do you get when seqret stops?  Could it just be that there is a malformed entry part way through your file?

Is the file you are trying to convert >2Gb in size?  If so this could be the reason for the failure rather than seqret being limited by the number of sequences.  In this case though I thought that the failure would happen when the file was first opened and not after a certain number of sequences had passed through.

If the problem is a large file you might be able to get round this by using a pipe to get information into seqret.  Try

cat your_genbank_file.gb | seqret -filter -osf gcg > your_gcg_file.gcg

This should work as long as your OS version of cat and your shell can handle large files.

Hope this helps


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