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MySQLandBLAST

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May 22nd, 2018
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Python 1.00 KB | None | 0 0
  1. from Bio.Blast import NCBIWWW
  2. from Bio.Blast import NCBIXML
  3. import mysql.connector
  4.  
  5. sequence = "CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGGAATAAA"
  6.  
  7. print("BLAST")
  8. result_handle = NCBIWWW.qblast("blastn","nr",sequence)
  9. print ("geBLAST")
  10. blast_record = NCBIXML.read(result_handle)
  11. print (blast_record)
  12.  
  13. cnx = mysql.connector.connect(user='owe4_bi1_3',password="blaat1234", host='127.0.0.1', database='owe4_bi1_3')
  14. cursor = cnx.cursor()
  15. for alignment in blast_record.alignments:
  16.     for hsp in alignment.hsps:
  17.         print ("Alignment")
  18.         print ("Sequence:", alignment.title)
  19.         print ("Length  :", alignment.length)
  20.         print ("e value :", hsp.expect)
  21.  
  22.         print (hsp.query[0:75])
  23.         print (hsp.match[0:75])
  24.         print (hsp.sbjct[0:75])
  25.         query_insert = "insert into blast_results values ('"+hsp.query[0:75]+"','"+hsp.match[0:75]+"','"+hsp.sbjct+"')"
  26.         print (query_insert)
  27.         cursor.execute (query_insert)
  28.         cursor.execute ("commit")
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