Hello Nail,
You need to reorder the columns of your csv file to match the Jalview features file format (as described at http://www.jalview.org/help/html/features/featuresFormat.html). If you are on Unix/OSX and have the awk command available, you could try this: awk -F',' -v OFS='\t' '{ print $2,$1,"-1",$4,$5,$3 }' P11169-coverage.csv > features.txt This writes out columns 2,1,4,5,3 of the csv to output file features.txt. * -F',' specifies comma as the field separator in the input file * OFS='\t' specifies tab as the field separator in the output file I was able to load the output as a features file in Jalview. Adapt as required! Reformatting the JSON file would be rather more work, or need a parser to be coded. Best regards, Mungo p.s. ignore last incomplete email. I shouldn't try to email from a moving bus! [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carsta...@dundee.ac.uk<mailto:g.m.carsta...@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ________________________________ From: Mungo Carstairs (Staff) Sent: 03 July 2019 08:32:00 To: Nail Besli; jalview-discuss@jalview.org Subject: Re: [Jalview-discuss] load annotations or future file Hello Nail, You need to reformat the columns of your csv file to match the Jalview features file format (as described at [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carsta...@dundee.ac.uk<mailto:g.m.carsta...@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ________________________________ From: Nail Besli <beslin...@gmail.com> Sent: 02 July 2019 13:37:50 To: Mungo Carstairs (Staff) Subject: Re: [Jalview-discuss] load annotations or future file Thank you all. I really appreciate. My spesific problem is that attached files are not able to load features/annotations in section of File in JALview 2.10.5. How can I cope with it. Should I modify these files format? On Tue, Jul 2, 2019 at 11:48 AM Mungo Carstairs (Staff) <g.m.carsta...@dundee.ac.uk<mailto:g.m.carsta...@dundee.ac.uk>> wrote: Hello Nail, I am sorry to hear you are having problems. An annotation or features file should be plain text format, not JSON. Please see the help pages in the application or at http://www.jalview.org/help/html/features/annotationsFormat.html http://www.jalview.org/help/html/features/featuresFormat.html The DAS service registry was unfortunately discontinued in 2015 (see https://www.dasregistry.org/), and DAS options will be removed in the forthcoming release of Jalview. However you can still fetch annotation from PDB, Uniprot and other EBI databases using the menu option "Web Service | Fetch DB References". I hope this helps. If you are still having problems, please let us know the version of Jalview you are running, any error messages seen ("Tools | Show Java Console"), and if possible email me the file(s) that fail to load. Best regards, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carsta...@dundee.ac.uk<mailto:g.m.carsta...@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ________________________________ From: jalview-discuss-boun...@jalview.org<mailto:jalview-discuss-boun...@jalview.org> <jalview-discuss-boun...@jalview.org<mailto:jalview-discuss-boun...@jalview.org>> on behalf of Nail Besli <beslin...@gmail.com<mailto:beslin...@gmail.com>> Sent: 01 July 2019 20:07:46 To: jalview-discuss@jalview.org<mailto:jalview-discuss@jalview.org> Subject: [Jalview-discuss] load annotations or future file I just would like to load annotations or future file with *.json. Every single time, it gives error loading file. Also, I showed `https://www.ebi.ac.uk/pdbe/pdbe-kb`<https://www.ebi.ac.uk/pdbe/pdbe-kb> as a resource to load the sequence future is das settings. But it doesn't work. pls help me with this problem Best The University of Dundee is a registered Scottish Charity, No: SC015096 The University of Dundee is a registered Scottish Charity, No: SC015096
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