Question: How To Extract All The Gene Names From A Chromosomal Region In Ensembl Using Pycogent?
1
gravatar for jynling89
3.8 years ago by
jynling8910
jynling8910 wrote:

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 ensembl chromosome • 1.3k views
ADD COMMENTlink modified 3.3 years ago by Biostar ♦♦ 10 • written 3.8 years ago by jynling8910
3
gravatar for cts
3.8 years ago by
cts1.4k
Pasadena
cts1.4k wrote:

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.

ADD COMMENTlink written 3.8 years ago by cts1.4k

Thanks, it worked.

ADD REPLYlink written 3.8 years ago by jynling8910
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