Consensus sequence extraction on ubuntu

Hi,

I'm using jalview on linux (ubuntu) platform and want to know how to extract consensus sequence from the alignment (right click and copy from consensus histogram option doesn't seems to work in the ubuntu)

Thanks for any help!

Best, Ganesh

Hi Ganesh

···

On 25/05/2015 14:40, Ganesh Phad wrote:

I'm using jalview on linux (ubuntu) platform and want to know how to extract consensus sequence from the alignment (right click and copy from consensus histogram option doesn't seems to work in the ubuntu)

Normally this does work (the option copies the consensus to the clipboard, for pasting into an alignment or another program).

Could you open the Jalview Java console (Tools->Show Java Console) and try to select the option again ? Please send me any output and I'll investigate (or you could open a bug at issues.jalview.org !).

Jim

Hi Jim,

Thanks, I tried but nothing happens when I right click on the histogram under the alignment, below is the java console output, please let me know what you think.

Thanks, Ganesh

Jalview Desktop Test
Build Date: unknown
Java version: 1.8.0_45
amd64 Linux 3.13.0-52-generic
DEBUG - find: resourceName='commons-logging.properties'
DEBUG - getNextResources: search using ClassLoader 'sun.misc.Launcher$AppClassLoader@4e25154f'
DEBUG - Could not find resource: commons-logging.properties
DEBUG - find: resourceName='org/apache/commons/logging/commons-logging.properties'
DEBUG - getNextResources: search using ClassLoader 'sun.misc.Launcher$AppClassLoader@4e25154f'
DEBUG - Could not find resource: org/apache/commons/logging/commons-logging.properties
DEBUG - find: serviceName = 'META-INF/services/org.apache.commons.logging.LogFactory'
DEBUG - find: resourceName='META-INF/services/org.apache.commons.logging.LogFactory'
DEBUG - getNextResources: search using ClassLoader 'sun.misc.Launcher$AppClassLoader@4e25154f'
DEBUG - Could not find resource: META-INF/services/org.apache.commons.logging.LogFactory
DEBUG - find: className='org.apache.commons.logging.impl.LogFactoryImpl'
DEBUG - getNextClass: next URL='jar:file:/usr/share/java/commons-logging.jar!/org/apache/commons/logging/impl/LogFactoryImpl.class'
DEBUG - loadClass: Loading class 'org.apache.commons.logging.impl.LogFactoryImpl' with sun.misc.Launcher$AppClassLoader@4e25154f
WARN - Exception when discovering One Way services:
WARN - Exception when discovering One Way services:
INFO - Not enabling Google Tracking.
INFO - Constructing news reader.
Discovered service: http://www.compbio.dundee.ac.uk/jabaws MafftWS
INFO - Completed construction of reader.
Discovered service: http://www.compbio.dundee.ac.uk/jabaws MuscleWS
Discovered service: http://www.compbio.dundee.ac.uk/jabaws ClustalWS
Discovered service: http://www.compbio.dundee.ac.uk/jabaws TcoffeeWS
Discovered service: http://www.compbio.dundee.ac.uk/jabaws ProbconsWS
INFO - Saved last read date as May 20, 2015 3:31:26 PM
INFO - Saved last read date as May 20, 2015 3:31:26 PM
INFO - Saved last read date as May 20, 2015 3:31:26 PM
Building ws menu again Thread[Thread-17,6,main]
Exception for url:http://www.dasregistry.org/das1/sources/
java.io.FileNotFoundException: http://www.dasregistry.org/das1/sources/
  at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1835)
  at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1440)
  at org.biojava.dasobert.das2.io.DasSourceReaderImpl.open(DasSourceReaderImpl.java:53)
  at org.biojava.dasobert.das2.io.DasSourceReaderImpl.readDasSource(DasSourceReaderImpl.java:65)
  at jalview.ws.DasSequenceFeatureFetcher.getDASSources(DasSequenceFeatureFetcher.java:865)
  at jalview.ws.DasSequenceFeatureFetcher.getDASSources(DasSequenceFeatureFetcher.java:848)
  at jalview.ws.SequenceFetcher.registerDasSequenceSources(SequenceFetcher.java:320)
  at jalview.ws.SequenceFetcher.<init>(SequenceFetcher.java:64)
  at jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(SequenceFetcher.java:118)
  at jalview.gui.AlignFrame$17.run(AlignFrame.java:4852)
  at java.lang.Thread.run(Thread.java:745)

···

________________________________________
From: Jim Procter [foreveremain@gmail.com] on behalf of Jim Procter [jprocter@compbio.dundee.ac.uk]
Sent: 25 May 2015 15:47
To: Ganesh Phad; jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] Consensus sequence extraction on ubuntu

Hi Ganesh

On 25/05/2015 14:40, Ganesh Phad wrote:

I'm using jalview on linux (ubuntu) platform and want to know how to extract consensus sequence from the alignment (right click and copy from consensus histogram option doesn't seems to work in the ubuntu)

Normally this does work (the option copies the consensus to the
clipboard, for pasting into an alignment or another program).

Could you open the Jalview Java console (Tools->Show Java Console) and
try to select the option again ? Please send me any output and I'll
investigate (or you could open a bug at issues.jalview.org !).

Jim

How did you install Jalview ? It looks like source build but no build date has been given. Could you try the version at

http://www.jalview.org/builds/release/webstart/jalview_2G.jnlp

Jim.

···

Sent from my android device.

-----Original Message-----
From: Ganesh Phad ganesh.phad@ki.se
To: Jim Procter jprocter@compbio.dundee.ac.uk, “jalview-discuss@jalview.orgjalview-discuss@jalview.org
Sent: Mon, 25 May 2015 18:02
Subject: RE: [Jalview-discuss] Consensus sequence extraction on ubuntu

Hi Jim,

Thanks, I tried but nothing happens when I right click on the histogram under the alignment, below is the java console output, please let me know what you think.

Thanks, Ganesh

Jalview Desktop Test
Build Date: unknown
Java version: 1.8.0_45
amd64 Linux 3.13.0-52-generic
DEBUG - find: resourceName=‘commons-logging.properties
DEBUG - getNextResources: search using ClassLoader ‘sun.misc.Launcher$AppClassLoader@4e25154f’
DEBUG - Could not find resource: commons-logging.properties
DEBUG - find: resourceName=‘org/apache/commons/logging/commons-logging.properties
DEBUG - getNextResources: search using ClassLoader ‘sun.misc.Launcher$AppClassLoader@4e25154f’
DEBUG - Could not find resource: org/apache/commons/logging/commons-logging.properties
DEBUG - find: serviceName = ‘META-INF/services/org.apache.commons.logging.LogFactory
DEBUG - find: resourceName=‘META-INF/services/org.apache.commons.logging.LogFactory
DEBUG - getNextResources: search using ClassLoader ‘sun.misc.Launcher$AppClassLoader@4e25154f’
DEBUG - Could not find resource: META-INF/services/org.apache.commons.logging.LogFactory
DEBUG - find: className=‘org.apache.commons.logging.impl.LogFactoryImpl
DEBUG - getNextClass: next URL=‘jar:file:/usr/share/java/commons-logging.jar!/org/apache/commons/logging/impl/LogFactoryImpl.class
DEBUG - loadClass: Loading class ‘org.apache.commons.logging.impl.LogFactoryImpl’ with sun.misc.Launcher$AppClassLoader@4e25154f
WARN - Exception when discovering One Way services:
WARN - Exception when discovering One Way services:
INFO - Not enabling Google Tracking.
INFO - Constructing news reader.
Discovered service: http://www.compbio.dundee.ac.uk/jabaws MafftWS
INFO - Completed construction of reader.
Discovered service: http://www.compbio.dundee.ac.uk/jabaws MuscleWS
Discovered service: http://www.compbio.dundee.ac.uk/jabaws ClustalWS
Discovered service: http://www.compbio.dundee.ac.uk/jabaws TcoffeeWS
Discovered service: http://www.compbio.dundee.ac.uk/jabaws ProbconsWS
INFO - Saved last read date as May 20, 2015 3:31:26 PM
INFO - Saved last read date as May 20, 2015 3:31:26 PM
INFO - Saved last read date as May 20, 2015 3:31:26 PM
Building ws menu again Thread[Thread-17,6,main]
Exception for url:http://www.dasregistry.org/das1/sources/
java.io.FileNotFoundException: http://www.dasregistry.org/das1/sources/
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1835)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1440)
at org.biojava.dasobert.das2.io.DasSourceReaderImpl.open(DasSourceReaderImpl.java:53)
at org.biojava.dasobert.das2.io.DasSourceReaderImpl.readDasSource(DasSourceReaderImpl.java:65)
at jalview.ws.DasSequenceFeatureFetcher.getDASSources(DasSequenceFeatureFetcher.java:865)
at jalview.ws.DasSequenceFeatureFetcher.getDASSources(DasSequenceFeatureFetcher.java:848)
at jalview.ws.SequenceFetcher.registerDasSequenceSources(SequenceFetcher.java:320)
at jalview.ws.SequenceFetcher.(SequenceFetcher.java:64)
at jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(SequenceFetcher.java:118)
at jalview.gui.AlignFrame$17.run(AlignFrame.java:4852)
at java.lang.Thread.run(Thread.java:745)


From: Jim Procter [foreveremain@gmail.com] on behalf of Jim Procter [jprocter@compbio.dundee.ac.uk]
Sent: 25 May 2015 15:47
To: Ganesh Phad; jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] Consensus sequence extraction on ubuntu

Hi Ganesh

On 25/05/2015 14:40, Ganesh Phad wrote:

I’m using jalview on linux (ubuntu) platform and want to know how to extract consensus sequence from the alignment (right click and copy from consensus histogram option doesn’t seems to work in the ubuntu)
Normally this does work (the option copies the consensus to the
clipboard, for pasting into an alignment or another program).

Could you open the Jalview Java console (Tools->Show Java Console) and
try to select the option again ? Please send me any output and I’ll
investigate (or you could open a bug at issues.jalview.org !).

Jim

Hi Jim,

I used a installer file (with java VM) available for linux platform from this link - http://www.jalview.org/Web_Installers/install.htm and then I think I had to download/install jdk, don't remember exactly, anyway, a new version you sent is working, I could copy the consensus sequence when I right click near the consensus name and not on the histogram so that's good. Thanks for a quick replies and help!

Best, G

···

From: Jim Procter [foreveremain@gmail.com] on behalf of jprocter@compbio.dundee.ac.uk [jprocter@compbio.dundee.ac.uk]
Sent: 25 May 2015 21:45
To: jalview-discuss@jalview.org; Ganesh Phad
Subject: RE: [Jalview-discuss] Consensus sequence extraction on ubuntu

How did you install Jalview ? It looks like source build but no build date has been given. Could you try the version at

http://www.jalview.org/builds/release/webstart/jalview_2G.jnlp

Jim.

Sent from my android device.

-----Original Message-----
From: Ganesh Phad <ganesh.phad@ki.se>
To: Jim Procter <jprocter@compbio.dundee.ac.uk>, "jalview-discuss@jalview.org" <jalview-discuss@jalview.org>
Sent: Mon, 25 May 2015 18:02
Subject: RE: [Jalview-discuss] Consensus sequence extraction on ubuntu

Hi Jim,

Thanks, I tried but nothing happens when I right click on the histogram under the alignment, below is the java console output, please let me know what you think.

Thanks, Ganesh

Jalview Desktop Test
Build Date: unknown
Java version: 1.8.0_45
amd64 Linux 3.13.0-52<tel:313052>-generic
DEBUG - find: resourceName='commons-logging.properties<http://commons-logging.properties>'
DEBUG - getNextResources: search using ClassLoader 'sun.misc.Launcher<http://sun.misc.Launcher>$AppClassLoader@4e25154<tel:25154>f'
DEBUG - Could not find resource: commons-logging.properties<http://commons-logging.properties>
DEBUG - find: resourceName='org/apache/commons/logging/commons-logging.properties<http://commons-logging.properties>'
DEBUG - getNextResources: search using ClassLoader 'sun.misc.Launcher<http://sun.misc.Launcher>$AppClassLoader@4e25154<tel:25154>f'
DEBUG - Could not find resource: org/apache/commons/logging/commons-logging.properties<http://commons-logging.properties>
DEBUG - find: serviceName = 'META-INF/services/org.apache.commons.logging.LogFactory<http://org.apache.commons.logging.LogFactory>'
DEBUG - find: resourceName='META-INF/services/org.apache.commons.logging.LogFactory<http://org.apache.commons.logging.LogFactory>'
DEBUG - getNextResources: search using ClassLoader 'sun.misc.Launcher<http://sun.misc.Launcher>$AppClassLoader@4e25154<tel:25154>f'
DEBUG - Could not find resource: META-INF/services/org.apache.commons.logging.LogFactory<http://org.apache.commons.logging.LogFactory>
DEBUG - find: className='org.apache.commons.logging.impl.LogFactoryImpl<http://org.apache.commons.logging.impl.LogFactoryImpl>'
DEBUG - getNextClass: next URL='jar:file:/usr/share/java/commons-logging.jar<http://commons-logging.jar>!/org/apache/commons/logging/impl/LogFactoryImpl.class<http://LogFactoryImpl.class>'
DEBUG - loadClass: Loading class 'org.apache.commons.logging.impl.LogFactoryImpl<http://org.apache.commons.logging.impl.LogFactoryImpl>' with sun.misc.Launcher<http://sun.misc.Launcher>$AppClassLoader@4e25154<tel:25154>f
WARN - Exception when discovering One Way services:
WARN - Exception when discovering One Way services:
INFO - Not enabling Google Tracking.
INFO - Constructing news reader.
Discovered service: http://www.compbio.dundee.ac.uk/jabaws MafftWS
INFO - Completed construction of reader.
Discovered service: http://www.compbio.dundee.ac.uk/jabaws MuscleWS
Discovered service: http://www.compbio.dundee.ac.uk/jabaws ClustalWS
Discovered service: http://www.compbio.dundee.ac.uk/jabaws TcoffeeWS
Discovered service: http://www.compbio.dundee.ac.uk/jabaws ProbconsWS
INFO - Saved last read date as May 20, 2015 3<tel:20153>:31:26 PM
INFO - Saved last read date as May 20, 2015 3<tel:20153>:31:26 PM
INFO - Saved last read date as May 20, 2015 3<tel:20153>:31:26 PM
Building ws menu again Thread[Thread-17,6,main]
Exception for url:http://www.dasregistry.org/das1/sources/
java.io.FileNotFoundException<http://java.io.FileNotFoundException>: http://www.dasregistry.org/das1/sources/
at sun.net.www.protocol.http.HttpURLConnection<http://sun.net.www.protocol.http.HttpURLConnection>.getInputStream0(HttpURLConnection.java:1835<http://HttpURLConnection.java:1835>)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream<http://sun.net.www.protocol.http.HttpURLConnection.getInputStream>(HttpURLConnection.java:1440<http://HttpURLConnection.java:1440>)
at org.biojava.dasobert.das2.io.DasSourceReaderImpl.open<http://org.biojava.dasobert.das2.io.DasSourceReaderImpl.open>(DasSourceReaderImpl.java:53<http://DasSourceReaderImpl.java:53>)
at org.biojava.dasobert.das2.io.DasSourceReaderImpl.readDasSource<http://org.biojava.dasobert.das2.io.DasSourceReaderImpl.readDasSource>(DasSourceReaderImpl.java:65<http://DasSourceReaderImpl.java:65>)
at jalview.ws.DasSequenceFeatureFetcher.getDASSources<http://jalview.ws.DasSequenceFeatureFetcher.getDASSources>(DasSequenceFeatureFetcher.java:865<http://DasSequenceFeatureFetcher.java:865>)
at jalview.ws.DasSequenceFeatureFetcher.getDASSources<http://jalview.ws.DasSequenceFeatureFetcher.getDASSources>(DasSequenceFeatureFetcher.java:848<http://DasSequenceFeatureFetcher.java:848>)
at jalview.ws.SequenceFetcher.registerDasSequenceSources<http://jalview.ws.SequenceFetcher.registerDasSequenceSources>(SequenceFetcher.java:320<http://SequenceFetcher.java:320>)
at jalview.ws.SequenceFetcher<http://jalview.ws.SequenceFetcher>.<init>(SequenceFetcher.java:64<http://SequenceFetcher.java:64>)
at jalview.gui.SequenceFetcher.getSequenceFetcherSingleton<http://jalview.gui.SequenceFetcher.getSequenceFetcherSingleton>(SequenceFetcher.java:118<http://SequenceFetcher.java:118>)
at jalview.gui.AlignFrame<http://jalview.gui.AlignFrame>$17.run<http://17.run>(AlignFrame.java:4852<http://AlignFrame.java:4852>)
at java.lang.Thread.run<http://java.lang.Thread.run>(Thread.java:745<http://Thread.java:745>)

________________________________________
From: Jim Procter [foreveremain@gmail.com<mailto:foreveremain@gmail.com>] on behalf of Jim Procter [jprocter@compbio.dundee.ac.uk<mailto:jprocter@compbio.dundee.ac.uk>]
Sent: 25 May 2015 15<tel:201515>:47
To: Ganesh Phad; jalview-discuss@jalview.org<mailto:jalview-discuss@jalview.org>
Subject: Re: [Jalview-discuss] Consensus sequence extraction on ubuntu

Hi Ganesh

On 25/05/2015 14:40, Ganesh Phad wrote:

I'm using jalview on linux (ubuntu) platform and want to know how to extract consensus sequence from the alignment (right click and copy from consensus histogram option doesn't seems to work in the ubuntu)

Normally this does work (the option copies the consensus to the
clipboard, for pasting into an alignment or another program).

Could you open the Jalview Java console (Tools->Show Java Console) and
try to select the option again ? Please send me any output and I'll
investigate (or you could open a bug at issues.jalview.org<http://issues.jalview.org> !).

Jim