Hi Leighton > From: Leighton Pritchard <lpr...@scri.ac.uk> > To: <artemis-users@sanger.ac.uk> > Subject: Issues with ARTEMIS/CHADO combination on OSX > > 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
The syntax is to give each database a name, e.g.: pi_broad 10.211.55.8:5432/pi_broad?lpritc \ > > * 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. For model A: chado_infer_CDS_UTR=no I'm not sure the tutorial is particularly clear. The model used here (in the pathogen group) uses gene, mRNA, exon, polypep and UTRs - this is model A (chado_infer_CDS_UTR=no) where the CDS is inferred. The second one stores just the gene, mRNA, exon and polypep - CDS & UTRs are then implicit. > * 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. Yes it isn't that smart at the moment when you view aa of the polypeptide. > > * 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). > I am guessing the mapping in artemis_sqlmap/Feature.xml needs to set the java type to string for the uniquename that you are using then. So you could try changing the template-basicfeature resultmap to: <result property="uniqueName" column="uniquename" javaType="java.lang.String"/> Regards Tim > 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 > _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
