Add antiSMASH and SequenceServer BLAST

fmalmeida / bacannot

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

https://bacannot.readthedocs.io/en/latest/

GNU General Public License v3.0

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Closed fmalmeida closed 2 years ago

fmalmeida commented 3 years ago

Add in a new release (v2.4) the following software:

Add antiSMASH annotation in order to provide additional insights about protein clusters in the input bacterial genomes.
- Must have TXT file outputs
- Must have a visualization in JBrowse
- Must have a specific RMarkdown report for antiSMASH
- This report must go inside the shiny app
Add a new tab in the shiny app in which users can easily execute the SequenceServer BLAST using the bacterial genome, proteins and genes.

fmalmeida commented 2 years ago

About implementations

antiSMASH (a beautiful html is automatically produced by antismash itself)
- [x] Implemented in "single genome analysis"
- [x] Included in JBrowse
- [x] Included the HTML report link in the shiny app
- [x] Implemented in "multiple genome analysis"
SequenceServer
- [x] Added to the shiny app

fmalmeida commented 2 years ago

antiSMASH + sequenceserver seems ready for release ...

Just needs to make sure everything is being properly loaded in the Jbrowse and Shiny app.

And finally make sure everything is properly added to documentation.

😄

fmalmeida commented 2 years ago

Bug found:

[x] antiSMASH creates subsets of the regions where the coordinates are not related to the main chromosome length, which is raising problems in putting these results to jbrowse since the "features" are all being placed in the start of sequence since their positions are being writen based on the subset sequences ...
[x] Also, the antiSMASH report is not being placed in the list of reports on the shiny app

fmalmeida commented 2 years ago

Done!

Now must only document the modules and finish the one related to resfinder (so all can come together):