Re: [Artemis-users] Customizing crunch file in ACT...
That's a wonderful idea. In fact I already load the contig's FT track (from Abacas's). But, it never occurred to me that we can modify it to load linker information as well. After Alex's email, I am started to wonder if the linkers are providing any value addition at all?. I will have to explore. Thanks very much Alex. Gowtham PS: Are you using Abacas by any chance Alex? If so, can I ask couple questions offline. Thanks. On 12/14/11 11:26 PM, Bossers, Alex alex.boss...@wur.nl wrote: Alternatively (as we do it) we generate an EMBL FT track containing the layout of contigs (incl any rev complementing and/or linkers). Works quite well for us and keeps comparison files clean/original. ALex -Oorspronkelijk bericht- Van: artemis-users-boun...@sanger.ac.uk [mailto:artemis-users-boun...@sanger.ac.uk] Namens Julian Parkhill Verzonden: woensdag 14 december 2011 9:42 Aan: Gowthaman Ramasamy CC: artemis-users@sanger.ac.uk Onderwerp: Re: [Artemis-users] Customizing crunch file in ACT... Gowthaman , The right hand scroll bar controls the display of links based on size of the hit (removing shorter hits up to 1kb). If you want to control the display based on the score, then right click in the centre window and select Set Score Cutoffs ... Julian. On 13 Dec 2011, at 23:20, Gowthaman Ramasamy wrote: Hi Everyone, I trying to trick ACT to display linking bars from two different blast out files. I have a chromosome at one side and newly scaffolded chromosome on the other side (generated by ordering of contigs using Abacas). I want to display two kinds of link between them. 1. crunch file from Abacas. To show matching/ordered contigs. So there will be only few super wide bars. 2. tblastx outfile between these chromosomes (used MSPcrunch to match with Abacas outfile output) I manually fuse both the files and use in ACT. It display links from both. But, I want to make abacas crunch disappear most of the time. My naïve attempt was to change score in the Abacas crunch file tozero artificially, so that I can block that link using the ACT 's middle window scroll bar. But, it does not respond. I mean, it does not control the display based on score. But, when I load un modified blastout file (with -m 9) option, it seems to control the display. Is it something a known issue. Better, yet, is there any better way to use two different crunch/blast out files? Gowthaman PS: I can load one chromosome twice. But, anything else? ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users Julian Parkhill Tel: +44(0)1223 494902 ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[Artemis-users] run_blastp error from Webstart
Hi Tim, A related question. I was able to set up a local blast database, and managed to configure .artemis_options file to customize artemis. It works when I use locally installed (linux) version of artemis. But, when I call Webstart version from sanger, it picks up the .artemis_options nicely (and displays custom db in Run-blastp menu). But, when I launch the blastp job, it opens a SSH login window. Is there a way to force run_blastp script to run locally. Or is it not allowed in webstart version? Log file pasted below. Thanks, Gowtham 06 Apr 06:36 - 1.6.0_22 06 Apr 06:36 - Apple Inc. 06 Apr 06:36 - /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home 06 Apr 06:36 - Mac OS X 06 Apr 06:36 - Max. Heap Memory / Mb: 834 06 Apr 06:36 - Starting application: Artemis 06 Apr 06:36 - Diana.ini not found 06 Apr 06:36 - options not found 06 Apr 06:36 - options.txt not found 06 Apr 06:36 - options.text not found 06 Apr 06:36 - /Users/gramasamy/.artemis_options options read 06 Apr 06:36 - Working directory: /Users/gramasamy while reading from LmjF.01.embl: misc_feature can't have ID as a qualifier 06 Apr 06:36 - PRODUCT STORED AS A CV (product_cv=yes) IN genedb_products 06 Apr 06:36 - SYNONYM NAMES ARE STORED IN genedb_synonym_type 06 Apr 06:36 - BAM VCF not visible 06 Apr 06:37 - WRITTEN /Users/gramasamy/Downloads/test/blastp/blastp_file_of_filenames.9 06 Apr 06:37 - GET READY TO CALL SSH CLIENT blastp 06 Apr 06:37 - CALL SSH CLIENT blastp 06 Apr 06:37 - WRITTEN /Users/gramasamy/Downloads/test/blastp/blastp_file_of_filenames.10 06 Apr 06:37 - GET READY TO CALL SSH CLIENT blastp 06 Apr 06:37 - CALL SSH CLIENT blastp while reading from LmjF.01.embl: misc_feature can't have ID as a qualifier 06 Apr 09:13 - BAM VCF not visible 06 Apr 09:13 - WRITTEN /Users/gramasamy/Downloads/test/blastp/blastp_file_of_filenames.11 06 Apr 09:13 - GET READY TO CALL SSH CLIENT blastp 06 Apr 09:13 - CALL SSH CLIENT blastp On 3/16/11 5:04 AM, Tim Carver t...@sanger.ac.uk wrote: Hi Leighton Actually using .artemis_options in the users home directory works on windows, or at least on the windows version I have tried it on here. To find where java thinks the user home directory is there is an application here: ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/util/JavaSystemProps. jar download and double clicking on this will print out the system properties. One of the properties is 'user.home' which the folder where Artemis should look for the .artemis_options file. I shall update the manual to reflect this. Regards Tim On 3/16/11 11:00 AM, Leighton Pritchard leighton.pritch...@scri.ac.uk wrote: Hi, Historically, of the places Artemis can look for an options file, only two were available on Windows (http://bioweb2.pasteur.fr/docs/artemis/art/options-chapt.html) - one requiring repacking of the artemis.jar file, and the other being to place the file in the folder containing the artemis.jar file. When using the Java Web Start version of Artemis on Windows, we can't really ask users to unpack and repack the artemis.jar file, but we can put an options.txt file in the Downloads folder that contains the artemis.jnlp file - this is a little volatile as a solution, though. On OSX the JWS version reads my .artemis_options file, happily. I may have missed it in the documentation, but is there another way to specify options when using Java Web Start for Artemis on Windows? Cheers, L. -- Dr Leighton Pritchard MRSC Plant Pathology Programme, SCRI (C block) Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA e:lpr...@scri.ac.uk w:http://www.scri.ac.uk/staff/leightonpritchard gpg/pgp: 0xFEFC205C tel: No telephone during office refurbishment [The James Hutton Institute logo] Please note that from 1 April 2011, SCRI and the Macaulay Land Use Research Institute will join to become The James Hutton Institute. __ SCRI, Invergowrie, Dundee, DD2 5DA. The Scottish Crop Research Institute is a charitable company limited by guarantee. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmas...@scri.ac.uk quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor
[Artemis-users] Command line options to load BAM files and zoom to a gene
Hi All, I am wondering if the following can be achieved by command line options alone. I would like to load a gff file (with sequences), and load two or more .bam files and to navigate to gene of interest. (controlling zoom level, if that is not too much to ask). As you might have guessed it from now, I would like to make the job of some scientists in our lab bit easier by pre-configuring everything. So, that they fire a command / click a link, they are taken to Artemis and to the region of their interest. So, if anyone has any other way to achieve it, i will really appreciate it.. Thanks so much in advance, Gowtham ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[Artemis-users] Command line options to load BAM files and zoom to a gene
Hi All, I am wondering if the following can be achieved by command line options alone. I would like to load a gff file (with sequences), and load two or more .bam files and to navigate to gene of interest. (controlling zoom level, if that is not too much to ask). As you might have guessed it from now, I would like to make the job of some scientists in our lab bit easier by pre-configuring everything. So, that they fire a command / click a link, they are taken to Artemis and to the region of their interest. So, if anyone has any other way to achieve it, i will really appreciate it.. Thanks so much in advance, Gowtham ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[Artemis-users] command line options
Hi All, I am wondering if the following can be achieved by command line options alone. I would like to load a gff file (with sequences), and load two or more .bam files and to navigate to gene of interest. (controlling zoom level, if that is not too much to ask). As you might have guessed it from now, I would like to make the job of some scientists in our lab bit easier by pre-configuring everything. So, that they fire a command / click a link, they are taken to Artemis and to the region of their interest. So, if anyone has any other way to achieve it, i will really appreciate it.. Thanks so much in advance, Gowtham ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[Artemis-users] Viewing next gen sequence reads on artemis
Hi Tim, I am trying to see if we can use artemis to display aligned illumina reads against a chromosome. I know we can make user plot and display coverage information. But wondering is there a way to display the reads themselves (nt seq). Gowtham ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[Artemis-users] Command line option to load data file for ACT
Hi Tim, I have a question about loading the files into ACT on command line. Without using file browser. Here is what I am trying to do. I would like to compare 5 genomes each having 35+ chormosomes. Some has more contigs. When the user want to see a gene in a reference genome I want to fire up ACT, with all the 5 genomes and their comparison files. I have a perl script which finds out the syntenic chromosomes and does a tblastx to make ACT compatible blastout files for all the 5 genomes. Now wondering is there an command line option so that I can automate the loading of all the information in to ACT. To avoid user loading 5 genome files, 5 annotation files and 3 comparison files everytime. Thanks very much for the time Happy Holidays. Gowtham ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[Artemis-users] Running local blast with Webstart Artemis
Hi All, I am able to configure my local Artemis installation to work with blast and local database. But, wondering, Can the same thing be done with web start artemis also. I understand, the path for the database can be set with RUN menu set options. How can I make it see the blastp and run_blastp scripts.. Thanks very much in advance, Gowthaman SBRI ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] Configuring Blast with Mac Art 11
That's Cool, Tim. Thanks. As mentioned in my earlier email I made blast to work under Linux Art11. Before I move to webstart and Jar files, I wanted to configure blast with Mac Art11. I did edit my run_blastp file under the etc directory and it works very well with command line. But, When I try to run it from main Artemis window, it is asking for login details (of what? The system?). But, it does not run blastall really. I don't see any output. Where am I going wrong? Any hints Tim?. I am attaching my run_blastp script hereonly change I made is for EXEC. For the database, I am giving the full path in the RUN-set menu option. That's how I did for my linux-Art11. Thanks once again for the reply, I really appreciate it. Gowtham SBRI (/run_blastp /Users/gramasamy/work/localartWD/blastp/blastp_file_of_filenames.4 /Applications/artemis/Artemis.app/Contents/blast-data/uniprot) Command line: works great, although complains as following..but does the JOB Error seen: Fatal server error: Server is already active for display 0 If this server is no longer running, remove /tmp/.X0-lock and start again. AbortDDX Quitting Xquartz... On 3/24/09 11:09 AM, Tim Carver t...@sanger.ac.uk wrote: Hi Gowthaman It can be done. You would need to unwrap your jar file and edit the run scripts that are in that. Then jar the contents back up. Alternatively, in the Artemis cvs there is a Makefile that can be used to make the jar files with: gmake jar Regards Tim On Tue, 24 Mar 2009, Gowthaman Ramasamy wrote: Hi All, I am able to configure my local Artemis installation to work with blast and local database. But, wondering, Can the same thing be done with web start artemis also. I understand, the path for the database can be set with RUN menu set options. How can I make it see the blastp and run_blastp scripts.. Thanks very much in advance, Gowthaman SBRI On 3/18/09 3:35 AM, Tim Carver t...@sanger.ac.uk wrote: Hi Rob You can find documentation for setting up blast/fasta and the databases in the Readme.txt in the MacOSX distribution. You can then edit the run_blast* scripts in Artemis.app/Contents/artemis/etc and options file if required as per the documentation in the manual: http://www.sanger.ac.uk/Software/Artemis/v11/manual/runmenu.html Regards Tim On 3/17/09 9:25 PM, Rob Good rtg...@unimelb.edu.au wrote: Can someone please point me to a link that will tell me how to configure run_blast, etc options for Macosx artemis. Rob Good Ph. +61 3 8344 2347 Genetics Dept University of Melbourne PARKVILLE, Australia ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users run_blastp Description: Binary data ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
[Artemis-users] can artemis lock/checkout a gene from chado
Hi all, I am working with the latest artemis (v10) working off the chado database. I'm wondering, If it can checkout and lock a gene so that other annotators do not make modifications to the same gene /region which will get lost when I commit it back to the database. Thanks, Gowtham ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
