[EMBOSS] Does seqret have limitations ?
simon andrews (BI)
simon.andrews at bbsrc.ac.uk
Tue Dec 16 16:46:39 UTC 2003
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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