get-CD.py: retrieve CD sequences

See #1801.
Note that we could also use XML or JSON from genenames.org : http://www.genenames.org/help/rest-web-service-help

germline/get-CD.py

+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+'''Get from NCBI CD sequences from the HCDM database (hcdm.org), as exported by HGNC (genenames.org)'''
+
+import urllib
+
+HUGO_REQUEST = 'http://www.genenames.org/cgi-bin/download?'
+HUGO_COLS = '&col=gd_hgnc_id&col=md_refseq_id&col=gd_other_ids_list&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=gd_pub_refseq_ids'
+
+# HUGO query on 'hcdm.org' entries
+HUGO_QUERY = '&status=Approved&status=Entry+Withdrawn&status_opt=2&where=gd_other_ids+LIKE+%27%25hcdm.org%25%27&order_by=gd_app_sym_sort&format=text&limit=&hgnc_dbtag=on&submit=submit'
+
+HUGO_URL = HUGO_REQUEST + HUGO_COLS + HUGO_QUERY
+
+NCBI_API = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=fasta&retmode=text'+'&id=%s'
+
+
+OUT = 'CD.fa'
+
+print "==>", OUT
+out = open(OUT, 'w')
+
+for l in urllib.urlopen(HUGO_URL).readlines():
+    ll = l.split('\t')
+
+    try:
+        hugo, ncbi, ids = ll[0], ll[1], ll[2]
+        cd_id = ids.split(',')[2].strip()
+    except:
+        print "!", l
+        continue
+        
+    print cd_id, hugo, ncbi 
+    
+    fasta = urllib.urlopen(NCBI_API % ncbi).read()
+    fasta_with_id = fasta.replace('>', '>%s|%s|' % (hugo, cd_id))    
+
+    out.write(fasta_with_id)
+
+    
+