ncbi.py: get_gene_position(), from eutils API

germline/ncbi.py

@@ -9,6 +9,10 @@ API_EUTILS = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?'
 API_NUCCORE_ID =         API_EUTILS + 'db=nuccore&rettype=fasta&retmode=text' + '&id=%s'
 API_NUCCORE_ID_FROM_TO = API_EUTILS + 'db=nuccore&rettype=fasta&retmode=text' + '&id=%s' + '&from=%s&to=%s'
 
+API_GENE_ID_XML = API_EUTILS + 'db=gene&retmode=xml&rettype=docsum' + '&id=%s'
+
+
+from xml.dom import minidom, Node
 
 
 
@@ -31,3 +35,34 @@ def ncbi_and_write(ncbi, additional_header, outs):
     for out in outs:
         out.write(fasta_with_id)
 
+
+
+# Parse output from API_GENE_ID_XML to get genomic positions of a gene
+
+def xml_bang_one(parent):
+    return {node.nodeName: node.firstChild.nodeValue for node in parent.childNodes if node.nodeType == Node.ELEMENT_NODE}
+
+def get_last_LocationHistType(gene):
+    '''
+    >>> get_last_LocationHistType(6969)
+    {u'AssemblyAccVer': u'GCF_000001405.38', u'ChrAccVer': u'NC_000007.14', u'AnnotationRelease': u'109', u'ChrStop': u'38253379', u'ChrStart': u'38253428'}
+    '''
+
+    sys.stderr.write('%% eutils -> gene %s' % gene + '\n')
+    xml = minidom.parseString(urllib.urlopen(API_GENE_ID_XML % gene).read())
+
+    locations = xml.getElementsByTagName('LocationHistType')
+    return xml_bang_one(locations[0])
+
+def get_gene_positions(gene):
+    '''
+    >>> get_gene_positions(6969)
+    (u'NC_000007.14', 38253428, 38253379)
+    '''
+
+    loc = get_last_LocationHistType(gene)
+
+    chr = loc['ChrAccVer']
+    start, stop = int(loc['ChrStart']), int(loc['ChrStop'])
+
+    return chr, start, stop