I wish to use an annotation file to decorate my alignment. I created a dummy file (below) and used File->Load Features/Annotations. The file is called features.txt.
I am greated with an error box saying that jalview,
“Couldn’t load file /tmp/features.txt
Formats currently supported are
Fasta, MSF, Clustal, BLC, PIR, MSP and Pfam”
Can someone enlighten me as to how I can load in my file? The alignment is displayed when I try this.
I am using Jalview 2.3 (though the about option says 6.1). I do the same thing. I load a .aln file (from clustalw) then from the alignment window in Jalview I choose Load Features/Annotations and it works. An example of the beginning of a features file (which I create automatically in a Java program):
dpa1 111111
d1gv1a1_O d1gv1a1 -1 6 6 dpa1
The main difference I see in my file versus yours (at least as included in the email) is that I used tabs and your snippet appears to have spaces between columns.
Note: I use the numeric designation of a color so that I can get gradations of the same color.
Judith
···
On Apr 25, 2008, at 12:09 PM, James Wasmuth wrote:
Hi All,
I wish to use an annotation file to decorate my alignment. I created a dummy file (below) and used File->Load Features/Annotations. The file is called features.txt.
I am greated with an error box saying that jalview,
“Couldn’t load file /tmp/features.txt
Formats currently supported are
Fasta, MSF, Clustal, BLC, PIR, MSP and Pfam”
Can someone enlighten me as to how I can load in my file? The alignment is displayed when I try this.
there was a space in the first line instead of a space . Fixed that and it works!
-james
···
On Fri, Apr 25, 2008 at 3:32 PM, Judith Cohn <jcohn@lanl.gov> wrote:
Hi,
I am using Jalview 2.3 (though the about option says 6.1). I do the same thing. I load a .aln file (from clustalw) then from the alignment window in Jalview I choose Load Features/Annotations and it works. An example of the beginning of a features file (which I create automatically in a Java program):
dpa1 111111
d1gv1a1_O d1gv1a1 -1 6 6 dpa1
The main difference I see in my file versus yours (at least as included in the email) is that I used tabs and your snippet appears to have spaces between columns.
Note: I use the numeric designation of a color so that I can get gradations of the same color.
Judith
On Apr 25, 2008, at 12:09 PM, James Wasmuth wrote:
Hi All,
I wish to use an annotation file to decorate my alignment. I created a dummy file (below) and used File->Load Features/Annotations. The file is called features.txt.
I am greated with an error box saying that jalview,
“Couldn’t load file /tmp/features.txt
Formats currently supported are
Fasta, MSF, Clustal, BLC, PIR, MSP and Pfam”
Can someone enlighten me as to how I can load in my file? The alignment is displayed when I try this.