Investigate ProtAnnot fail to load Lotmaria passim genes

To replicate the issue in IGB:
1) Select the Lotmaria passim genome in the Species menu and the L_passim_Apr_2014 Genome Version.
2) Navigate to Contig_1:81,219-95,810
3) Install ProtAnnot: Plug-ins > Launch App Manager > ProtAnnot > click Install
4) In IGB, select the gene in view.
5) Select Tools > Start ProtAnnot

This issue is due to the Lotmaria passim annotation bed files being improperly formatted (missing or incorrect columns). Supreeth is in the process of correcting all of the annotation files and then we will need to update them on the Quickload.

Supreeth has fixed the various annotation files and sent them to me. I need to test them, gzip/tabix index, and then push them to the Quickload.

Files have been pushed to subversion repository.

See IGBF-1617 for notes on how to test.

Irvin Naylor - please check that the functionality mentioned above is correctly implemented in IGB 9.1.6, the released version of IGB. Please make a note of any problems you may observe.

Followed the steps in IGB 9.1.6 and can confirm that functionality is working correctly. The console is showing no errors.

Attached is the console log. From my understanding, everything looks fine but I'll attach just in case

I can confirm that the functionality is working, but I am concerned by what I'm seeing in the log. I will investigate to see what is going on.

The log warnings are caused by an off by one error. I am working to correct the error in all of the files.

[~aloraine] - I have committed the updated annotation files to the subversion repository following testing on my local machine.

I no longer receive the console log referring to "lengths disagree" that was seen in Irvin's logs for the example above. However, while I have corrected the off by one error and so most annotations should now be correctly divisible by 3, there is still a subset of the annotations that is not. I double-checked with the original data from geneious and this is not a mistake, but possibly just poor annotation. It looks like several methods/tools were used to generate the annotations and one of them was more prone to create annotations that were not divisible by 3.

The other warning that Irvin saw in his logs refers to the name field being too long. I think this warning can be ignored as it does not seem to have any impact.

Current task - Quickloads need to be uploaded to reflect the changes to the Lotmaria passim files in the SVN repository.

Tested using lorainelab-quickload.scidas.org
The off by one error is no longer present.

[~aloraine] - igbquickload.org still has the older version of the annotation. Can I close this issue or wait until igbquickload.org has also been updated?

Updated igbquicload.org:

[aloraine@cci-vm12 quickload]$ svn up
U    L_passim_Apr_2014/CDS_Crithidia.bed.gz.tbi
U    L_passim_Apr_2014/Exon_Crithidia.bed.gz.tbi
U    L_passim_Apr_2014/gene_Crithidia.bed.gz.tbi
U    L_passim_Apr_2014/match_Crithidia.bed.gz
U    L_passim_Apr_2014/Protein_match_Crithidia.bed.gz
U    L_passim_Apr_2014/mRNA_Crithidia.bed.gz
U    L_passim_Apr_2014/Expressed_sequence_match_Crithidia.bed.gz
U    L_passim_Apr_2014/CDS_Crithidia.bed.gz
U    L_passim_Apr_2014/Exon_Crithidia.bed.gz
U    L_passim_Apr_2014/Protein_match_Crithidia.bed.gz.tbi
U    L_passim_Apr_2014/match_Crithidia.bed.gz.tbi
U    L_passim_Apr_2014/mRNA_Crithidia.bed.gz.tbi
U    L_passim_Apr_2014/gene_Crithidia.bed.gz
U    L_passim_Apr_2014/Expressed_sequence_match_Crithidia.bed.gz.tbi
Updated to revision 148.

Same at "renci" quickload.

Updated. Moving to "Needs Testing"

I am able to open and run ProtAnnot without the reported errors. Tested on macOS.