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By: a guest on May 11th, 2012  |  syntax: Python  |  size: 1.16 KB  |  hits: 15  |  expires: Never
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  1. from Bio.Blast import NCBIWWW
  2. from Bio.Blast import NCBIXML
  3.  
  4. best = open("malaria.txt","r")
  5. totaal = 0
  6. f1 = open("blast_report_found.txt","w")
  7. f2 = open("blast_report_notfound.txt","w")
  8. for r in best:
  9.     try:
  10.         totaal += 1
  11.         res_handle = NCBIWWW.qblast ("blastp", "nr", r)
  12.         print "Resultaat gevonden:",totaal
  13.  
  14.         record = NCBIXML.read(res_handle)
  15.  
  16.  
  17.  
  18.         for alignment in record.alignments:
  19.             for hsp in alignment.hsps:
  20.                 E_VALUE_THRESH = 10
  21.                 if hsp.expect < E_VALUE_THRESH:
  22.                   f1.write('****Alignment****\n')
  23.                   f1.write('result: '+alignment.title+'\n')
  24.                   f1.write('length: '+str(alignment.length)+'\n')
  25.                   f1.write('e value: '+str(hsp.expect)+'\n')
  26.                   f1.write(hsp.query[0:75] + '...\n')
  27.                   f1.write(hsp.match[0:75] + '...\n')
  28.                   f1.write(hsp.sbjct[0:75] + '...\n\n')
  29.         print "Resultaat weggeschreven voor nummer",totaal
  30.     except:
  31.         f2.write(r)
  32.  
  33. f1.close()
  34. f2.close()
  35. print "Alle resultaten zijn weggeschreven in blast_report_found.txt en blast_report_notfound.txt"
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