How To Extract All The Gene Names From A Chromosomal Region In Ensembl Using Pycogent?

Question

[jynling89]

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.

Answer 1

[cts]

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.

[jynling89]

Thanks, it worked.