| UGENE Forum | |
|
https://forum.ugene.net/forum/YaBB.pl
General Category >> Bugs and Issues >> genbank file format https://forum.ugene.net/forum/YaBB.pl?num=1365000373 Message started by randolf on Apr 3rd, 2013 at 9:46pm |
|
|
Title: genbank file format Post by randolf on Apr 3rd, 2013 at 9:46pm
Hi there,
I have a problem with the way ugene saves files in gb-fileformat: I use version 1.11.5 64amd Here step by step to reproduce the bug: I download a file (AL663079) from genbank in gb-format: The first line of the file is as followes: LOCUS AL663079 119796 bp DNA linear ROD 13-DEC-2012 Now I add an annotation in ugene and save the file, the first line is now: LOCUS AL663079 119796 bp DNA linear ROD 03-APR-2013 The problem now is that there is only one white space between bp and DNA. Now I can not open the file with biopython. Biopython complains that the file does not conform to the file format specifications. When I change the LOCUS line of the new file to 4 white space between bp and DNA and 5 whitespace between DNA and linear, like in the original file, the new file works again with biopython. So I suggest, that ugene should not change the spacing in the LOCUS line. Cheers, Thomas |
|
Title: Re: genbank file format Post by Yuriy Vaskin on Apr 4th, 2013 at 1:53pm
Thank you, Thomas.
We have fixed that (https://ugene.unipro.ru/tracker/browse/UGENE-1584). Improved genbank writer will be available in UGENE 1.12 |
|
UGENE Forum » Powered by YaBB 2.5 AE! YaBB Forum Software © 2000-2010. All Rights Reserved. |