Download specific human DNA sequences from hg19

get_hg19_sequence.py

"""
get_hg19_sequence.py
Jamie Heather, February 2017
For use on Python 2.7, requires urllib2 module
"""

import urllib2

def get_hg19_seq(chrm, seq_from, seq_to):
    """
    Takes a chromosome number or name (1-22, X/Y/M) and two coordinates (from/to)
    Returns the corresponding hg19 nucleotide sequence via the UCSC DAS server.
    """
    base_url = "http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chr"
    page = urllib2.urlopen(base_url + str(chrm) + ":" + str(seq_from) + "," + str(seq_to))
    contents = []
    for line in page:
        if "<" not in line:
            contents.append(line.rstrip())
    full_seq = "".join(contents).upper()
    return full_seq