SEA-PHAGES | Release of Starterator version 1.2

Link to this post \| posted 15 Nov, 2019 21:24
cdshaffer	This is to announce the release of Starterator version 1.2 This release has some graphical updates and incorporates cluster information into the text reporting. The cluster information can be particularly helpful for large complex phams but has little or no value for small phams comprised of a single cluster. The new version will be used to create all online pham reports starting with database version 233 which should be posted to the web based pham reports the afternoon of Nov 15th. For anyone still using the virtual machine the new version will be made available soon for download and update (details to be posted soon). The main new features in this update: 1. Tracks now display only that region of the genes with starts, and, if the tracks are judged to be highly complex, the image is further zoomed in to show only the region surrounding called start sites 2. Tracks are now grouped by subcluster and the color of the track changes with each subcluster (Thanks for the idea go to Sally Molloy) 3. Cluster information of each phage is now added to the "Summary by Start" section (Thanks for the feature request go to Claire Rinehart) 4. A new "Summary by cluster" section has been added to give info on manual annotations specifically for each cluster found in the pham 5. Details on the number of manual annotations (MA's) for each start in a gene are now given in the "Gene information" section. Also added to the whole phage report (available if you still run starterator in a VM): 6. A new summary table on the analysis of manual annotations of pham members and the degree of consensus with the annotated start. 7. Simplified reporting focusing on the relevant results for the phage in the whole phage report 8. Support for parsing of the "CDS function" file exported from Pecaan when using the whole unphamerated phage analysis

Link to this post | posted 15 Nov, 2019 21:24

This is to announce the release of Starterator version 1.2

This release has some graphical updates and incorporates cluster information into the text reporting. The cluster information can be particularly helpful for large complex phams but has little or no value for small phams comprised of a single cluster. The new version will be used to create all online pham reports starting with database version 233 which should be posted to the web based pham reports the afternoon of Nov 15th. For anyone still using the virtual machine the new version will be made available soon for download and update (details to be posted soon).

The main new features in this update:

1. Tracks now display only that region of the genes with starts, and, if the tracks are judged to be highly complex, the image is further zoomed in to show only the region surrounding called start sites
2. Tracks are now grouped by subcluster and the color of the track changes with each subcluster (Thanks for the idea go to Sally Molloy)
3. Cluster information of each phage is now added to the "Summary by Start" section (Thanks for the feature request go to Claire Rinehart)
4. A new "Summary by cluster" section has been added to give info on manual annotations specifically for each cluster found in the pham
5. Details on the number of manual annotations (MA's) for each start in a gene are now given in the "Gene information" section.

Also added to the whole phage report (available if you still run starterator in a VM):
6. A new summary table on the analysis of manual annotations of pham members and the degree of consensus with the annotated start.
7. Simplified reporting focusing on the relevant results for the phage in the whole phage report
8. Support for parsing of the "CDS function" file exported from Pecaan when using the whole unphamerated phage analysis

Link to this post \| posted 16 Nov, 2019 13:00
debbie	WooHoo! Thanks Chris.

Link to this post \| posted 21 Nov, 2019 16:20
edgingtonn1	Awesome Chris–Thanks!

Link to this post \| posted 10 Dec, 2019 22:20
smolloy123	you're a genius Chris!

Link to this post \| posted 11 Dec, 2019 01:44
scaruso	Been using it, and it's great! Steve

Link to this post \| posted 04 Aug, 2020 14:47
scaruso	Chris, Just installed the new version of the VM for genome checking and I'm running into two problems that might be related. I'm having trouble updating Phamerator the first time and Starterator 1.2 won't run. It just closes. I assume that's because the Phamerator DB isn't getting set up? Does that make sense? Steve

Link to this post \| posted 04 Aug, 2020 15:18
scaruso	Chris, OK, so I can see the Actino_Draft DB, but starterator 1.2 still won't run at all. Just stalls and then closes. Is that what it does when updating, like when there are no results from the old one? Or is there an issue in my VM? Or user error? Thanks, Steve

Link to this post \| posted 04 Aug, 2020 16:41
scaruso	Update - That must be in. It still works on the old VM, but not the new VM. So I'm not sure why, something weird is going on. Steve

Link to this post \| posted 04 Aug, 2020 16:55
cdshaffer	These issues are likely due to the changes in the database structure that have been released over the past few months. Sorry but I have just not had time to get the changes to Starterator in good enough shape to "publish" them as a new release. There are currently two options: 1. if you want a whole phage report just send me the name of the phage (if it is in phagesdb) or send me a DNA Master file (if it is not in phagesdb). I can easily run these on my "experimental" version of Starterator. 2. change your VM so it runs the experimental version of starterator. Briefly, to do this you need to pull the cdshaffer/phambymatch branch from my cdshaffer github repository and change phamerator preferences to a different server location so get the version of the phamerator database that is compatible with the phambymatch version of Starterator. If you are interested in that let me know I can easily provide more detailed command line instructions for doing the changes to get the experimental version of Starterator and how to change phamerater.

Link to this post | posted 04 Aug, 2020 16:55

cdshaffer

These issues are likely due to the changes in the database structure that have been released over the past few months. Sorry but I have just not had time to get the changes to Starterator in good enough shape to "publish" them as a new release. There are currently two options:
1. if you want a whole phage report just send me the name of the phage (if it is in phagesdb) or send me a DNA Master file (if it is not in phagesdb). I can easily run these on my "experimental" version of Starterator.
2. change your VM so it runs the experimental version of starterator. Briefly, to do this you need to pull the cdshaffer/phambymatch branch from my cdshaffer github repository and change phamerator preferences to a different server location so get the version of the phamerator database that is compatible with the phambymatch version of Starterator. If you are interested in that let me know I can easily provide more detailed command line instructions for doing the changes to get the experimental version of Starterator and how to change phamerater.

Link to this post \| posted 04 Aug, 2020 17:01
cdshaffer	it is probably working on the old VM because you have not run phamerator so you are on an old (pre-udpates) version of the database. It is important to remember that Starterator does not do all the database checking and management, it relies on the old phamerator to do that. So if you are using a VM you should always run phamerator 1st to get the most recent database and then run starterator.

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Release of Starterator version 1.2