def get_sequence_from_location(species, coords):
"""Get sequence from a genomic location in an ensembl species genome."""
from cogent.db.ensembl import HostAccount, Genome, Compara, Species
genome = Genome(Species=species, Release='87', account=None)
chrom, start, end, strand = coords
#print coords
r = genome.getRegion(CoordName=str(chrom),
Start=start,
End=end,
Strand=strand)
return r.Seq
def get_chrom_seqs(species, release, account=None, debug=False):
"""yields sequence objects for the indicated chromosomes from Ensembl"""
genome = Genome(species, Release=release, account=account)
for chrom in chroms[species]:
region = genome.getRegion(CoordName=chrom)
seq = region.Seq
name = 'chr_%s' % chrom
seq.Name = name
if debug:
print name
print repr(seq)
yield seq