[Next-Generation Sequencing Book]

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[ Ticket #1207 ] Errors in writing GenBank files
Date:
01/06/16 15:47
Submitted by:
B_Fristensky 		Assigned to:
B_Fristensky
Category:
bioLegato 		Priority:
5
Ticket group:
Bug 		Resolution:
Resolved
Summary:
Errors in writing GenBank files
Original submission:
BioLegato adds extra junk when writing GenBank files. eg.

1) Blank line between LOCUS and DEFINITION lines.
LOCUS SEG_LSTISF 6396 bp DNA linear PLN 25-AUG-2010

DEFINITION Lactuca sativa.
ACCESSION AH005956
VERSION AH005956.1 GI:2981179

2) Superfluous ORIGIN line indented

/note="region B; 3' flanking region of T-DNA insertion
site"
ORIGIN
1
ORIGIN
1 aagcttgtga atctatttcc gcgcaatccc atgtctctgt tgcatcatct tgaagagctt

To reproduce:

bldna --> File --> View sequences --> GenBank --> Run
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Followups
Comment Date By
This did indeed turn out to be a bug in readseq. A note has been sent to Don Gilbert to fix the problem, which is in the most recent versions: 2.1.27 and 2.1.30.

In the meantime, the simplest workaround is to deal with the problem only where it matters. Most programs don't care about these differences. Individual BioLegato menus will be fixed to deal with these few cases. It would be a lot of work to write a general script, because it would have to check both input and output formats before deciding whether to run readseq. 		01/13/16 20:16 B_Fristensky
A test of READSEQ at the command line shows that this is actually a bug in READSEQ, not in BioLegato. 01/13/16 19:06 B_Fristensky
This may actually be a bug in READSEQ, which is called
by View sequences. The workaround would be to write a
script that leaves the file alone if it's GenBank
format, and filters it through READSEQ for other formats. 		01/06/16 16:03 B_Fristensky
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Ticket change history
Field Old value Date By
status_id Open 01/13/16 20:16 B_Fristensky
resolution_id Not Resolved 01/13/16 20:16 B_Fristensky
close_date 12/31/69 19:00 01/13/16 20:16 B_Fristensky
status_id Pending 01/06/16 15:47 B_Fristensky
assigned_to unset 01/06/16 15:47 B_Fristensky
resolution_id Unset 01/06/16 15:47 B_Fristensky

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