SEA-PHAGES | Starterator version 1.1 released

Link to this post \| posted 02 Dec, 2016 23:08
cdshaffer	Everyone, I am happy to announce the release of version 1.1 of Starterator. This has several minor updates and bug fixes. It is available now from github.com/SEA-PHAGES/starterator. I have let Dan know and I expect he aleady has or will very soon the new SEA 2017 VM to this new version. I will be collaborating with Dan to create an update script which can be run to update the Starterator currently installed on a working VM. New features: 1. Better recognition of identical tracks which are then collapsed into a single track. Many phams now have significantly fewer tracks. 2. Tracks are now labeled with the name of the first phage on the list and indicate how many other phage are also represented in the track 3. Tracks now indicate the called start with a yellow bar if the start is Draft quality and a green bar if the start is based on published annotations 4. The report has been updated in several ways: A. The report now indicates the start which has been most often called in the published annotations and does not consider draft quality annotations when looking for the "most annotated" start. B. The "suggested starts" section has been depreciated as it was too often based on draft annotations which simply perpetuated the original Glimmer/Genemark calls. C. The run date has been added to the output so that changes in the phamerator database can be easily recognized and the most recent report used for analysis. 5. Many minor bugfixes We will post update info for those that wish to continue to use older VM's soon.

Link to this post | posted 02 Dec, 2016 23:08

Everyone,
I am happy to announce the release of version 1.1 of Starterator. This has several minor updates and bug fixes. It is available now from github.com/SEA-PHAGES/starterator. I have let Dan know and I expect he aleady has or will very soon the new SEA 2017 VM to this new version.
I will be collaborating with Dan to create an update script which can be run to update the Starterator currently installed on a working VM.

New features:
1. Better recognition of identical tracks which are then collapsed into a single track. Many phams now have significantly fewer tracks.
2. Tracks are now labeled with the name of the first phage on the list and indicate how many other phage are also represented in the track
3. Tracks now indicate the called start with a yellow bar if the start is Draft quality and a green bar if the start is based on published annotations
4. The report has been updated in several ways:
A. The report now indicates the start which has been most often called in the published annotations and does not consider draft quality annotations when looking for the "most annotated" start.
B. The "suggested starts" section has been depreciated as it was too often based on draft annotations which simply perpetuated the original Glimmer/Genemark calls.
C. The run date has been added to the output so that changes in the phamerator database can be easily recognized and the most recent report used for analysis.

5. Many minor bugfixes

We will post update info for those that wish to continue to use older VM's soon.

Link to this post \| posted 15 Dec, 2016 16:22
edgingtonn1	Awesome! Thanks Chris!

Link to this post \| posted 08 Jan, 2017 02:27
lhughes	Hi Chris, When I tried running a couple of phage on the v.1.1 version, I got an crash error after just a few phams (8 on one and 5 on the other). Both the phage I tried were BD1 phages (BeardedLady and Oliynyk). I switched back to the v.1.1.1Beta and everything seems to run fine. Thoughts? Lee

Link to this post \| posted 10 Jan, 2017 02:34
cdshaffer	Curious, It is entirely possible there is a bug in the code that I added when going to v1.1 from the that beta version. I tested my most recent version and it did not crash on beardedlady. Unfortunately I am in the middle of updating the part of starterator that generates the pdf report. I got most of the issues with the single pham reports the way I want them but I have not updated the code to handle the "all phage" reports. I have posted the most recent version of a whole phage report here: phages.wustl.edu/BeardedLady_DraftReport.pdf but you can see there is still a lot I need to add back into the reports before they are useful again. It does have all the graphics tracks its just missing all the summary reports on annotated starts and all that. If you just use the graphical tracks the whole report should work, if you want all the text summary you will just have to stick with the beta version or go to phages.wustl.edu/starterator and get the pham report for each pham in the phage one by one.

Link to this post | posted 10 Jan, 2017 02:34

cdshaffer

Curious,
It is entirely possible there is a bug in the code that I added when going to v1.1 from the that beta version. I tested my most recent version and it did not crash on beardedlady. Unfortunately I am in the middle of updating the part of starterator that generates the pdf report. I got most of the issues with the single pham reports the way I want them but I have not updated the code to handle the "all phage" reports. I have posted the most recent version of a whole phage report here:

phages.wustl.edu/BeardedLady_DraftReport.pdf

but you can see there is still a lot I need to add back into the reports before they are useful again. It does have all the graphics tracks its just missing all the summary reports on annotated starts and all that.

If you just use the graphical tracks the whole report should work, if you want all the text summary you will just have to stick with the beta version or go to phages.wustl.edu/starterator and get the pham report for each pham in the phage one by one.

Link to this post \| posted 10 Jan, 2017 04:17
lhughes	Thanks, Chris. I think we'll be fine with the Beta version for now. Lee

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Starterator version 1.1 released