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Not all motifs are retrieved if fetched by species? #3

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IanKouzel opened this issue Oct 8, 2024 · 0 comments
Open

Not all motifs are retrieved if fetched by species? #3

IanKouzel opened this issue Oct 8, 2024 · 0 comments

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@IanKouzel
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Hi,

First of all, thanks for the great interface to access and download JASPAR TF motif profiles!

I am particularly interested in one TF (NRF1) that I am not able to retrieve with pyJASPAR using 'species' argument like this:

jdb_obj.fetch_motifs(collection="CORE", species=["9606"])

It can be retrieved by downloading TFs for taxonomic group, i.e. 'Vertebrates':

motifs = jdb_obj.fetch_motifs(
...         collection = ['CORE'],
...         tax_group = ['Vertebrates'],
...         all_versions = False)

However, then there is a mix of human and non-human TF motifs, and I need purely human TF motifs.

It is possible to fetch it by id:

jdb_obj.fetch_motif_by_id('MA0506.1')

Is there any workaround to get all human TF motifs including NRF1 in one function call or do I do anything wrong when fetching the motifs?

Kind regards,
Ian

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