Subprocess fails to catch the standard output

Question

I am trying to generate tree with fasta file input and Alignment with MuscleCommandline

import sys,os, subprocess
from Bio import AlignIO
from Bio.Align.Applications import MuscleCommandline
cline = MuscleCommandline(input="c:\Python26\opuntia.fasta")
child= subprocess.Popen(str(cline),
                         stdout = subprocess.PIPE,
                         stderr=subprocess.PIPE,
                        shell=(sys.platform!="win32"))
align=AlignIO.read(child.stdout,"fasta")
outfile=open('c:\Python26\opuntia.phy','w')
AlignIO.write([align],outfile,'phylip')
outfile.close()

I always encounter with these problems

Traceback (most recent call last):
  File "<string>", line 244, in run_nodebug
  File "C:\Python26\muscleIO.py", line 11, in <module>
    align=AlignIO.read(child.stdout,"fasta")
  File "C:\Python26\Lib\site-packages\Bio\AlignIO\__init__.py", line 423, in read
    raise ValueError("No records found in handle")
ValueError: No records found in handle

Answer 1

You have an unprotected backslash in your output filename, that is never good.

Use 'r' to get raw strings, i.e. r'c:\Python26\opuntia.phy'.

Answer 2

I mean line

align=AlignIO.read(child.stdout,"fasta") is not working with exceptions.ValueError: No records found in handle

Answer 3

From the documentation of the subproccess library:

Warning

Use communicate() rather than .stdin.write, .stdout.read or .stderr.read to avoid deadlocks due to any of the other OS pipe buffers filling up and blocking the child process.

so maybe you could try something like:

mydata = child.communicate()[0]

Answer 4

Still encounter error at line --align=AlignIO.read(child.communicate()[0],"fasta")

import sys,os, subprocess

from Bio import AlignIO

from subprocess import Popen, PIPE

from Bio.Align.Applications import MuscleCommandline

cline = MuscleCommandline(input="c:\Python26\opuntia.fasta")

child= subprocess.Popen(str(cline),

                     stdout = subprocess.PIPE,

                     stderr=subprocess.PIPE,

                    shell=(sys.platform!="win32"))

align=AlignIO.read(child.communicate()[0],"fasta")

outfile=open(r"c:\Python26\opuntia.phy","w")

AlignIO.write([align],outfile,'phylip')

outfile.close()

I dont know why i am facing too much problem with this subprocess

Answer 5

Biopython 1.54 was released today with a stable version of the Bio.Phylo module. I've updated the documentation with an example pipeline for generating trees. For simplicity, the example uses ClustalW to align sequences and generate a tree, instead of Muscle and Phylip, but most of the code is still the same or similar.

http://biopython.org/wiki/Phylo#Example_pipeline

If you've already generated a tree with Phylip (using the .phy alignment as input), you can still follow the Phylo examples in general. Phylip creates a Newick file with a name like "outttree" or "foo.tree".

(Feel free to merge this with Brad's answer; I can't write a comment in that thread yet.)