Saving output of a for-loop to file

Question

I have opened a file with blast results and printed out the hits in fasta format to the screen.

The code looks like this:

result_handle = open(\"/Use         


        

Answer 1

you can use with statement to ensure that file will be closed

from __future__ import with_statement

with open('/Users/jonbra/Desktop/my_blast.xml', 'w') as outfile:
    from Bio.Blast import NCBIXML
    blast_records = NCBIXML.parse(result_handle)
    blast_record = blast_records.next()
    for alignment in blast_record.alignments:
        for hsp in alignment.hsps:
            outfile.write('>%s\n%s\n' % (alignment.title, hsp.sbjct))

or use try ... finally

outfile = open('/Users/jonbra/Desktop/my_blast.xml', 'w')
try:
    from Bio.Blast import NCBIXML
    blast_records = NCBIXML.parse(result_handle)
    blast_record = blast_records.next()
    for alignment in blast_record.alignments:
        for hsp in alignment.hsps:
            outfile.write('>%s\n%s\n' % (alignment.title, hsp.sbjct))
finally:
    outfile.close()