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
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