python, fetch sequence from DAS by coordinates

Question

ucsc DAS server, which get DNA sequences by coordinate.

URL: http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chr20:30037432,30038060

sample file:

<DASDNA>
  <SEQUENCE id="chr20" start="30037832" stop="30038060" version="1.00">
  <DNA length="229">
    gtggcacccaaagatgctggaatctttatggcaaatgccgttacagatgc            
    tccaagaaggaaagagtctatgtttactgcataaataataaaatgtgctg     
    cgtgaagcccaagtaccagccaaaagaaaggtggtggccattttaactgc 
    tttgaagcctgaagccatgaaaatgcagatgaagctcccagtggattccc 
    acactctatcaataaacacctctggctga
  </DNA>
  </SEQUENCE>
</DASDNA>

what I want is this part:

    gtggcacccaaagatgctggaatctttatggcaaatgccgttacagatgc            
    tccaagaaggaaagagtctatgtttactgcataaataataaaatgtgctg     
    cgtgaagcccaagtaccagccaaaagaaaggtggtggccattttaactgc 
    tttgaagcctgaagccatgaaaatgcagatgaagctcccagtggattccc 
    acactctatcaataaacacctctggctga

I want to get the sequence part from thousands of this kind urls, how should i do it? I tried to write the data to file and parse the file, it worked ok, but is there any way to parse the xml-like string directly? i tried some example from other posts, but they didn't work.

Here, I added my solution. Thanks to the 2 answers below.

Solution 1:

def getSequence2(chromosome, start, end):
    base = 'http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment='
    url = base + chromosome + ':' + str(start) + ',' + str(end)
    doc = etree.parse(url,parser=etree.XMLParser())
    if doc != '':
        sequence = doc.xpath('SEQUENCE/DNA/text()')[0].replace('\n','')
    else:
        sequence = 'THE SEQUENCE DOES NOT EXIST FOR GIVEN COORDINATES'
    return sequence

Solution 2:

def getSequence1(chromosome, start, end):
    base = 'http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment='
    url = base + chromosome + ':' + str(start) + ',' + str(end)
    xml = urllib2.urlopen(url).read()
    if xml != '':
        w = open('temp.xml', 'w')
        w.write(xml)
        w.close()
        dom = parse('temp.xml')
        data = dom.getElementsByTagName('DNA')
        sequence = data[0].firstChild.nodeValue.replace('\n','')
    else: 
        sequence = 'THE SEQUENCE DOES NOT EXIST FOR GIVEN COORDINATES'
    return sequence

Of course they will need to import some necessary libraries.

Answer 1

>>> from lxml import etree
>>> doc = etree.parse("http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chr20:30037432,30038060",parser=etree.XMLParser())
>>> doc.xpath('SEQUENCE/DNA/text()')
['\natagtggcacatgtctgttgtcctagctcctcggggaaactcaggtggga\ngagtcccttgaactgggaggaggaggtttgcagtgagccagaatcattcc\nactgtactccagcctaggtgacagagcaagactcatctcaaaaaaaaaaa\naaaaaaaaaaaaaagacaatccgcacacataaaggctttattcagctgat\ngtaccaaggtcactctctcagtcaaaggtgggaagcaaaaaaacagagta\naaggaaaaacagtgatagatgaaaagagtcaaaggcaagggaaacaaggg\naccttctatctcatctgtttccattcttttacagacctttcaaatccgga\ngcctacttgttaggactgatactgtctcccttctttctgctttgtgtcag\ngtggcacccaaagatgctggaatctttatggcaaatgccgttacagatgc\ntccaagaaggaaagagtctatgtttactgcataaataataaaatgtgctg\ncgtgaagcccaagtaccagccaaaagaaaggtggtggccattttaactgc\ntttgaagcctgaagccatgaaaatgcagatgaagctcccagtggattccc\nacactctatcaataaacacctctggctga\n']

Answer 2

Use a Python XML parsing library like lxml, load the XML file with that parser, and then use a selector (e.g. using XPath) to grab the node/element that you need.