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("/Users/jonbra/Desktop/my_blast.xml")

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:
        print  > , alignment.title
        print hsp.sbjct

This outputs a list of fasta files to the screen. But how can I create a file and save the fasta output to this file?

Update: I guess I would have to replace the print statements within the loop with something.write(), but how will the > , alignment.title we written?

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
  % (alignment.title,))
f.write( %s
  % (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
"%alignment.title)
      f.write(hsp.sbjct+"
")

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

Answer 3

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
%s
  % (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
%s
  % (alignment.title, hsp.sbjct))
finally:
    outfile.close()

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

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
"%alignment.title)
            f.write(hsp.sbjct+"
")

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