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rsa-tools / rsat-code

This repo contains the code required to run a local version of the software suite Regulatory Sequence Analysis Tools (RSAT).
http://rsat.eu
GNU Affero General Public License v3.0
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link to external motif collection (ie footprintDB) from peak-motifs HTML tabular output #37

Closed eead-csic-compbio closed 1 year ago

eead-csic-compbio commented 1 year ago

Hi @morganeTC @jvanheld @najlaksouri , just added a simple function, sub MotifExternalURL, which adds hyperlinks to external motif collections within the tabular HTML output produced by peak-motifs. It only has an effect if the user requests comparing the motifs found by peak-motifs to motif databases. For the moment it works only for footprintDB, but can be extended to other motif databases in the future.

What this does is it contructs a URL using the motif name (field 'name2') if it comes from an enabled database. The URL opens in a new tab. If this fails it simply returns the original motif name and the first column in the table will be text-only (default).

In the case of footprintDB results this greatly facilitates browsing the annotated transcription factors known to bind to a particular motif and to the relevant papers, see the links in the column 'name' in the screenshot below:

imagen

morganeTC commented 1 year ago

Hi Bruno, it is an excellent idea. Note that Walter is actively working on peak-motifs2, and it may be interesting to exchange about how he has implemented this in the new version.

eead-csic-compbio commented 1 year ago

Hi Bruno, it is an excellent idea. Note that Walter is actively working on peak-motifs2, and it may be interesting to exchange about how he has implemented this in the new version.

@santanaw let me know if you need help replicating this in peak-motifs2

eead-csic-compbio commented 1 year ago

@morganeTC does the code seem ok to you, can you see any reason this can break? Can you review it please?

santanaw commented 1 year ago

Hi Bruno, it is an excellent idea. Note that Walter is actively working on peak-motifs2, and it may be interesting to exchange about how he has implemented this in the new version.

@santanaw let me know if you need help replicating this in peak-motifs2

Thank you @eead-csic-compbio. I will let you know if something pops out.