How To Extract All The Gene Names From A Chromosomal Region In Ensembl Using Pycogent?
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9.0 years ago
jynling89 ▴ 10

I would like to know if PyCogent modules can be used to extract all the gene names from a chromosomal region in Ensembl Database. If not, are there other alternatives to perform gene names extraction from Ensembl? Thanks.

gene chromosome ensembl • 2.5k views
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9.0 years ago
cts ★ 1.7k

I believe this is possible in pycogent. Looking at the code there is the getFeatures method of the cogent.db.ensembl.genome.Genome class (see the code snippet below).

def getFeatures(self, region=None, feature_types=None, where_feature=None,
                CoordName=None, Start=None, End=None, Strand=None,
                ensembl_coord=False):
    """returns Region instances for the specified location"""

I assume that you can pass it the coordinates using the Start and End kwargs.

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Thanks, it worked.

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