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

First, create a file object:

f = open("myfile.txt", "w") # Use "a" instead of "w" to append to file

You can print to a file object:

print >> f, '>', alignment.title
print >> f, hsp.sbjct 

Or you can write to it:

f.write('> %s\n' % (alignment.title,))
f.write('%s\n' % (hsp.sbjct,))

You can then close it to be nice:

f.close()

Answer 2

Something like this

with open("thefile.txt","w") as f
  for alignment in blast_record.alignments:
    for hsp in alignment.hsps:
      f.write(">%s\n"%alignment.title)
      f.write(hsp.sbjct+"\n")

prefer not to use print >> as that won't work anymore in Python3

Answer 3

for some reason the code above posted by OP did not work for me.. I modified a bit

from Bio.Blast import NCBIXML
f = open('result.txt','w')
for record in NCBIXML.parse(open("file.xml")) :
    for alignment in record.alignments:
        for hsp in alignment.hsps:
            f.write(">%s\n"%alignment.title)
            f.write(hsp.sbjct+"\n")

Answer 4

There are two general approaches. Outside of python:

python your_program.py >output_file.txt

Or, inside of Python:

out = open("output_file.txt", "w")
for alignment in blast_record.alignments:
    for hsp in alignment.hsps:
        print >>out, '>', alignment.title
        print >>out, hsp.sbjct
out.close()

Answer 5

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()