Hi, We've noticed the following issues with using ARTEMIS in conjunction with CHADO on OSX, recently (most recent ARTEMIS, SVN version of CHADO). With apologies for providing more in the way of bug reports...
* When setting up user options, they don't seem to be recognised correctly by the startup dialogue box. For example, specifying the following databases in ~/.artemis_options chado_servers = \ 10.211.55.8:5432/pi_broad?lpritc \ 10.211.55.8:5432/chado?chado Results in the "Available databases" dropdown box in the "Enter Database Address" dialogue presenting the two options: Default pi_broad Selecting 'pi_broad' populates the dialogue box with the information for the 'chado' database. Selecting 'Default' produces the default information. Removing the 'chado' database from the options file, leaving only 'pi_broad', throws the error: $ ./art -Dibatis -Dchado reading options from "/Users/lpritc/.artemis_options" Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 1 at uk.ac.sanger.artemis.components.database.DatabaseLoginPrompt.getServerComboB ox(DatabaseEntrySource.java:519) at uk.ac.sanger.artemis.components.database.DatabaseLoginPrompt.<init>(Database EntrySource.java:429) at uk.ac.sanger.artemis.components.database.DatabaseEntrySource.setLocation(Dat abaseEntrySource.java:161) at uk.ac.sanger.artemis.components.filetree.LocalAndRemoteFileManager.<init>(Lo calAndRemoteFileManager.java:161) at uk.ac.sanger.artemis.components.filetree.LocalAndRemoteFileManager.<init>(Lo calAndRemoteFileManager.java:61) at uk.ac.sanger.artemis.components.ArtemisMain.readArgsAndOptions(ArtemisMain.j ava:287) at uk.ac.sanger.artemis.components.ArtemisMain$9.run(ArtemisMain.java:786) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEvent(EventQueue.java:633) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java :296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:21 1) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java :201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) * We use the gene, mRNA, exon, five_prime_UTR, etc. model named as model A at http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial - the tutorial says that the option chado_infer_CDS_UTR=yes Is required to change the default model to model B. However, our five_prime_UTR features are only respected if we set chado_infer_CDS_UTR=no Which the tutorial says should set model B, which lack five_prime_UTRs. Is the tutorial incorrect? It doesn't seem entirely consistent with the CHADO administration document from the Sanger site, but I could be misreading one or the other. * Inferred polypeptide features report the wrong amino acid sequence via the context menu. For example, for the 3-exon feature: supercont1.10 artemis exon 1192203 1192571 . - . ID=7000003035152080:CDS;Parent=7.00000303515208E15 supercont1.10 artemis exon 1192062 1192128 . - . ID=7000003035152080:CDS;Parent=7.00000303515208E15 supercont1.10 artemis exon 1191516 1191988 . - . ID=7000003035152080:CDS;Parent=7.00000303515208E15 A single polypeptide feature is inferred supercont1.10 PI_T3-4_FINAL_CALLGENES_3.coords polypeptide 1191516 1192571 . - . ID=auto106194;Name=polypeptide-auto106194;Derives_from=7.00000303515208E15;N ote=polypeptide+feature+inferred+from+GFF3+CDS+feature;isObsolete=false;feat ure_id=106194;feature_relationship_rank=0;timelastmodified=19.04.2010+04:41: 20+BST;translation=MLDPRETFSGVMGAFCCVYAGLPFEVVKVRLQTQGSKNAYTGVSDAFRRIATEEGLF ALWKGAVPALSSSIIENSVLFSANGVAKRAVLTLHAKQRAAHEGEYQLTTLDEALMGAFSGCFSATAITVPENIKC KLQFQRGHLGEGRYHGPWDCLMKVGKEEGITGLFRGYSALLLRDVPFSFFFFGSYQAFTSGSAKLLGNESKNDLNP AAILASGGLAGATSWGIMFPVDVLKSRMQTASSTGPLSLRGAFRAVYSEFGIHGFYRGWSAAVLRAFPANGSLFLG VEMTHRVFRWLDARHAV what has the correct translation. However, using the context menu to view the translation (right click -> view -> amino acids of selection) naively translates the single strand between the polypeptide feature limits. * Where the parent feature of another feature has a long digit value as its identifier, it is reported in the child feature by ARTEMIS in exponential float format, rather than as a string (see exon examples above). Cheers, L. -- Dr Leighton Pritchard MRSC D131, Plant Pathology Programme, SCRI 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:+44(0)1382 562731 x2405 ______________________________________________________ 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. 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