TChan/Notebook/2007-3-20
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BLAST SNP XML to OMIM
- NOTE: This probably doesn't work - will tweak when I can get a sample xml file to work with.
from Bio.EUtils import DBIdsClient import xml.dom.minidom from xml.dom.minidom import parse, parseString # From SNP BLAST xml to OMIM (using Xiaodi's code as a template...and then just using his code :)) # C-style struct to pass parameters class rsID: pass # queries the database and returns all info in an XML format def BLAST_SNP_search(sample_seq): client = DBIdsClient.DBIdsClient() query = client.search(sample_seq, "BLAST SNP") records = [i.efetch(rettype="xml") for i in query] return records # basic text extraction from XML; based on http://docs.python.org/lib/dom-example.html def get_text(node_list): rc = "" for node in node_list: if node.nodeType == node.TEXT_NODE: rc = rc + node.data return rc # extracts allelic variant data, as the name implies, using the struct above def extract_rsID(): dom = parseString() rsIDs = dom.getElementsByTagName("gn1|dbSNP|") if len(rsIDs) == 0: return parsed = [] for rs in rsIDs: b = rsID() # create empty instance of struct # now populate the struct b.rsIDnum = get_text(rs.getElementsByTagName("gn1|dbSNP|")[0].childNodes) parsed.append(a) return parsed seq = open('sample_sequence.txt') rsID_array = [] for i in BLAST_SNP_search(seq): b = extract_rsID(i.read()) if rsIDs != None: for b in rsIDs: rsID_array.append(b.rsIDnum) print b.rsIDnum # C-style struct to pass parameters class AllelicVariant: pass # queries the database and returns all info in an XML format def omim_snp_search(dnsnp_id): client = DBIdsClient.DBIdsClient() query = client.search(dnsnp_id, "omim") records = [i.efetch(rettype="xml") for i in query] return records # basic text extraction from XML; based on http://docs.python.org/lib/dom-example.html def get_text(node_list): rc = "" for node in node_list: if node.nodeType == node.TEXT_NODE: rc = rc + node.data return rc # extracts allelic variant data, as the name implies, using the struct above def extract_allelic_variant_data(str): dom = parseString(str) variants = dom.getElementsByTagName("Mim-allelic-variant") if len(variants) == 0: return parsed = [] for v in variants: a = AllelicVariant() # create empty instance of struct # now populate the struct a.name = get_text(v.getElementsByTagName("Mim-allelic-variant_name")[0].childNodes) a.mutation = get_text(v.getElementsByTagName("Mim-allelic-variant_mutation")[0].getElementsByTagName("Mim-text_text")[0].childNodes) a.description = get_text(v.getElementsByTagName("Mim-allelic-variant_description")[0].getElementsByTagName("Mim-text_text")[0].childNodes) parsed.append(a) return parsed for j in rsID_array: for i in omim_snp_search(rsID_array[j]): v = extract_allelic_variant_data(i.read()) if v != None: for a in v: print a.name print a.mutation print a.description