Blast Results Wont Return

Question

[Harpal]

This isnt my usual way if doing things but because im using Plone it has to be done this way.

The function below takes a variable "x" which is the query sequence. Its is then formatted to a blast-able format and then blasted against the database. When results are retuned the file is empty. Any idea why? I had this working but now its not...

def print_query(x):
    f = open('/home/rv/ncbi-blast-2.2.23+/db/test.txt', 'w')
    f.write(x)
    from subprocess import Popen
    Popen(["formatdb", "-p", "T", "-i", "/home/rv/ncbi-blast-2.2.23+/db/test.txt"])
    Popen(["blastall", "-d", "/home/rv/ncbi-blast-2.2.23+/db/vdatabase.fasta", "-i", "/home/rv/ncbi-blast-2.2.23+/db/test.txt", "-p", "blastp", "-m", "8", "-e", "0.01", "-o", "/home/rv/ncbi-blast-2.2.23+/db/output.blast"])
    return open('/home/rv/ncbi-blast-2.2.23+/db/output.blast', 'r').read()

P.S. I know im using the outdated BLAST I'm planning on switching when i have this working

Answer 1

[Istvan Albert]

The culprit is most likely that you are not waiting for the Popen process to finish.

There are several alternatives that you can try, the simplest being:

subprocess.call(*popenargs, **kwargs)

Docs say: Run command with arguments. Wait for command to complete, then return the returncode attribute.

But it is probably best if you first consult the documentation for the subprocess module.

PS: also make sure to close the open filehandle before the Popen call:

f.close()

[Istvan Albert]

There is no need to call sleep explicitly. The subprocess.call() will wait for the process to finish. So would the wait() method on the popen object.

[brentp]

The simplest might be just to add .wait() to the end of the 2 lines that start with "Popen"

[Craig]

Would time.sleep() work?