Hello,
Can we calculate the consensus sequence from the command line(Linux system) with no display?.
Thanks and Regards
Kajal
Hi Kajal - we don't have a convenient command line switch to do this, but it is possible using a groovy script. Save the following to a file:
// export a consensus sequence
def alf = Jalview.getAlignFrames();
for (ala in alf)
{
// ala is an jalview.gui.AlignFrame object
jalview.datamodel.SequenceI seq = ala.viewport.getConsensusSeq();
print new jalview.io.FastaFile().print(((jalview.datamodel.SequenceI) [ seq ]),false)+"\n";
}
Assuming you are using the conda package then you can execute the script via:
jalview -headless -groovy exportconsensus.groovy -open myalignment.fa
Jim.
PS. Apologies for the scruffy coding ! I'm sure someone can improve on the script's syntax 
PPS. If you are processing lots of alignments it may be worth launching a single Jalview instance as a server and sending it commands. You could also run Jalview from a Jupyter notebook with beaker-x.
PPS. Issue lodged here: https://issues.jalview.org/browse/JAL-3547
···
On 03/03/2020 05:11, kajal pande wrote:
Hello,
Can we calculate the consensus sequence from the command line(Linux system) with no display?.Thanks and Regards
Kajal_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
Hello again, Kajal - I've added the groovy script to Jalview's script directory, so it will be published in the next Jalview release.
You can download it directly via the commit linked to this issue:
https://issues.jalview.org/browse/JAL-3547
https://source.jalview.org/crucible/browse/jalview/examples/groovy/exportconsensus.groovy?r=89baab96128b7c469bae27a4ae7a0c870292f507
Jim.
···
On 03/03/2020 08:31, Jim Procter wrote:
Hi Kajal - we don't have a convenient command line switch to do this, but it is possible using a groovy script. Save the following to a file:
// export a consensus sequence
def alf = Jalview.getAlignFrames();
for (ala in alf)
{
// ala is an jalview.gui.AlignFrame object
jalview.datamodel.SequenceI seq = ala.viewport.getConsensusSeq();print new jalview.io.FastaFile().print(((jalview.datamodel.SequenceI) [ seq ]),false)+"\n";
}
Assuming you are using the conda package then you can execute the script via:
jalview -headless -groovy exportconsensus.groovy -open myalignment.fa
Jim.
PS. Apologies for the scruffy coding ! I'm sure someone can improve on the script's syntax
PPS. If you are processing lots of alignments it may be worth launching a single Jalview instance as a server and sending it commands. You could also run Jalview from a Jupyter notebook with beaker-x.
PPS. Issue lodged here: https://issues.jalview.org/browse/JAL-3547On 03/03/2020 05:11, kajal pande wrote:
Hello,
Can we calculate the consensus sequence from the command line(Linux system) with no display?.Thanks and Regards
Kajal_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss