Error passing generated fasta to blastn in biopython

Question

[Daniel]

I'm running a script which finds regions of interest, outputs them to a fasta, then passes them to blastn. Both steps work independently, but the script wont wait for the file to be generated and says:

./seq_targeter.py -i ecoli.fa -o tester -B
Testing if regions match guidelines.
Running blastn for all generated sequences.
('', 'Warning: [blastn] Query is Empty!\n')
All done, see files: tester-table.txt, tester.fasta and tester.bln

The script is basically this:

def main():
    outfasta = open(args.o + ".fasta", 'w')  
    seqTargeter(outfasta)               # Outputs a fasta file as expected
    blastFunc(args.o + ".fasta")      # Outputs a blank file and gives error above

seqTargeter(outfasta):
    print "Testing if regions match guidelines."
    .................
    outfasta.write('...........')

def blastFunc(blastfasta):
    print "Running blastn for all generated sequences."
    blastn_cline = NcbiblastnCommandline(query=blastfasta, db=args.d, outfmt=7, out=args.o + ".bln")()
    print blastn_cline

If I comment out the seqTargeter parts and let the script run on the already generated output.fasta file, then blastn will be called correctly and give the correct output. But if I want them both to work after the other, then nothing. I've been looking at something like this from Stackexchange, but I think the file exists doesn't work as it's still being generated...

Thanks

[Jenez]

Reposted comment as answer.

[Daniel]

Perfect, totally what I'd missed. If you put this as an answer I could accept it.

Answer 1

[Jenez]

outfasta = open(args.o + ".fasta", 'w')

It's never closed again from what I see. The file content will not be properly written unless you close the file. Even if this is not the issue, try to use with open(file, 'w') as out: instead as it will close itself properly.