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Is it possible to programmaticaly (e.g. using the ... #6493

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wormbasehelp opened this issue Jul 3, 2018 · 2 comments
Closed

Is it possible to programmaticaly (e.g. using the ... #6493

wormbasehelp opened this issue Jul 3, 2018 · 2 comments

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@wormbasehelp
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@wormbasehelp wormbasehelp commented Jul 3, 2018

Help Desk query collected when no chat operators were online. Follow up required.

Is it possible to programmaticaly (e.g. using the restAPI) fetch gene sequences with the case preserved for exons (upper) and introns (lower) as per the sequence pop-up widget? If not is there somewhere I can download all the C. elegans genes with the preserved case?

Reported by: Dami************* (dami************)
Submitted from: https://wormbase.org/about/userguide/for_developers#423015--10
Browser: Firefox 60.0

@sibyl229

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@sibyl229 sibyl229 commented Jul 19, 2018

The user is contacted:

The sequence popup has the same content as the sequence widget of a transcript page or a CDS page, so you can get the relevant infomation through the REST API for those widgets. For example:

curl https://www.wormbase.org/rest/widget/cds/B0336.6/sequences?content-type=application/json
curl https://wormbase.org/rest/widget/transcript/B0336.6.1/sequences?content-type=application/json

Currently, you can find the sequence in the JSON response under the print_sequence field. You will need to use some regular expression to remove the HTML tags. You might also be interested in the predicted_exon_structure field.

@raymond91125

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@raymond91125 raymond91125 commented Jul 30, 2018

To be considered as helped?

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