Extending MapMan Ontology to Tobacco for Visualization of Gene Expression

Listing 1

Processing BLAST XML to comma-delimited file.

from Bio.Blast import NCBIXML

expect_threshold = 1e-9

outfile = open('blast_output.txt', 'w')

for record in NCBIXML.parse(open('blast_output.xml')):

  query_title = record.query.split()[ 0 ]

  query_length = float(record.query_length)

  for alignment in record.alignments:

    for hsp in alignment.hsps:

      if float(hsp.expect) < expect_threshold:

        data = [query_title,

           alignment.title.split()[ 1 ].split('.')[ 0 ],

           str(float(hsp.identities)/query_length),

           str(query_length),

           str(hsp.expect)]

        outfile.writelines(','.join(data) + '⧵n')

outfile.close()