Hello Rachel, thanks for your email.
Hi,
I am a new user to Jalview.
I would like to pull out the conservation information from a multiple sequence alignment using the command line.
I'm afraid there's no easy way of doing this from the command line
without some kind of additional coding - however, read on.
I have installed Jalview via the java webstart.
when I use the command line arguments:
-open cfos.fasta -nodisplay -jalview out.txt
I get an application error. 'unable to launch application' and these details:
InvalidArgumentException[ Invalid arguments supplied: {out.txt, http://www.jalview.org/webstart/jalview.jnlp }]
at com.sun.javaws.Main.launchApp(Unknown Source)
at com.sun.javaws.Main.continueInSecureThread(Unknown Source)
at com.sun.javaws.Main$1.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
This is a problem with the version of webstart that you are using - and
the Jalview FAQ needs to be updated to reflect this. Many versions of
webstart now do not parse on the remaining arguments to the
application's main method. If you want to run jalview from the command
line, the simplest route is to download the jars from here:
http://www.jalview.org/webstart/
and then, assuming you have a working java on your path, and after first
replacing $WSDIR with the directory where you saved the jars, use the
following command:
java -djava.ext.dirs=$WSDIR jalview.bin.Jalview (command line args...)
How can I use the command line version of jalview to create the jalview output containing conservation
information without manually running jalview and exporting?
the above should be sufficient to execute the 'output as Jalview project
file' command that you suggest above. I presume you already have the
necessary parser to extract the annotation from the jalview XML file.
all the best - I hope this helps
Jim.
ยทยทยท
Rachel.Hawken@csiro.au wrote: