Hello,
When I load the sequence features file with 'File-Load Features/Annotations' it is not applied to my sequence, but it is loaded as an additional alignment (Jalview 2.8, Windows 7). My feature file is shown below:
···
--------------------------
grade0 FFFF96
grade1 10C8D1
grade2 8CFFFF
grade3 D7FFFF
grade4 EAFFFF
grade5 FFFFFF
grade6 FCEDF4
grade7 FAC9DE
grade8 F07DAB
grade9 A02560
ConSurf 2Q06/1-475 -1 1 1 grade2
ConSurf 2Q06/1-475 -1 2 2 grade5
ConSurf 2Q06/1-475 -1 3 3 grade7
....
....
-----------------------------------------------------
As a result, I have new sequences called grade0, grade1 etc. I also tried the command line:
jalview -fasta myAlignment.fa -features myFeatures.txt
But this does not even show the alignment, the Jalview program starts up without any error message (also no error in the Java console window), but no sequences were loaded.
I would be grateful for any advice.
Many thanks
Andreas
Hi Andreas.
When I load the sequence features file with 'File-Load Features/Annotations' it is not applied to my sequence, but it is loaded as an additional alignment (Jalview 2.8, Windows 7).
That's usually a sign that Jalview did not recognise the file as a GFF or jalview features file. Please make sure you are using tabs to separate each field in each line.
You should also not be including the /Start-End in the sequence ID field for the features file. If you have any more problems, then feel free to send me your file and an example alignment so I can see what's going on.
Jim.
ps.
jalview -fasta myAlignment.fa -features myFeatures.txt
Here the -fasta parameter should be -open (Jalview recognises input filetype automatically) .. you only use the -<output format> switches if you want to write out the alignment in a different format. In this case, you don't see a message because Jalview quits immediately since no alignment was specified.
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On Tue Jul 16 10:24:39 2013, Kukol, Andreas wrote: