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I have many scRNAseq datasets saved as hdf5 files, and when I open them keys sometimes are confused, so I need a way of determining from string values themselves whether the array contains gene symbols or ensembl ids. What would be a regular expression in python to check for it?

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Fixed it myself actually, not that hard. I found regular expression for ensembl ids here:

https://www.biostars.org/p/99142/

And used the re package in python:

import re

ensembl_regexp = 'ENS[A-Z]+[0-9]{11}'

is_ensembl = np.all([bool(re.match(ensembl_regexp, gene)) for gene in gene_symbols])
    if is_ensembl:
        gene_symbols = list(f['ensembl_ids']) 

Where gene_symbols is a numpy array that I need to check whether it has ensembl ids, and if yes, switch to using gene symbols which are going to be under ensembl_ids key due to a mistake of someone who made the hdf5 dataset.

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  • $\begingroup$ What kind of Ensembl IDs are matched by the second part of that regex? ENS[A-Z]+[0-9]{11} matches the standard Ensembl IDs, what does the rest do? It looks like it matches FlyBase IDs (CG[0-9]+), and all sorts of other things. For example, that regex would consider CG1 or ABC123bobbie valid Ensembl IDs. $\endgroup$ – terdon Sep 2 '18 at 11:13
  • $\begingroup$ Not sure, that’s what I got from the ‘Biostars’ link that is present in the answer. Maybe ask the person who answered it on ‘Biostars’ ? $\endgroup$ – Nikita Vlasenko Sep 2 '18 at 20:34
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    $\begingroup$ Is this your question originally? Did you test this solution? The regex matches all sorts of IDs, many of which are not Ensembl. I have edited your answer so that it only matches Ensembl IDs as the question asks for. $\endgroup$ – terdon Sep 3 '18 at 8:22
  • $\begingroup$ Of course, this is still not entirely correct since it will allow something like ENSABCDEFGHIJKL12345678901 which is clearly not a valid ID. $\endgroup$ – terdon Sep 3 '18 at 9:30

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