TypeError: Can't convert 'bytes' object to str implicitly using Python3.5

April 16, 2018, at 00:34 AM

I am using Python 3.5 on the following code.

def raxml(DIR,cleaned,num_cores,seqtype):
        assert cleaned.endswith(".aln-cln"),\
                "raxml infile "+cleaned+" not ends with .aln-cln"
        assert seqtype == "aa" or seqtype == "dna","Input data type: dna or aa"
        assert len(read_fasta_file(DIR+cleaned)) >= 4,\
                "less than 4 sequences in "+DIR+cleaned
        clusterID = cleaned.split(".")[0]
        tree = DIR+clusterID+".raxml.tre"
        raw_tree = "RAxML_bestTree."+cleaned
        model = "PROTCATWAG" if seqtype == "aa" else "GTRCAT"
        if not os.path.exists(tree) and not os.path.exists(raw_tree):
                # raxml crashes if input file starts with . 
                infasta = cleaned if DIR == "./" else DIR+cleaned
                cmd = ["raxml","-T",str(num_cores),"-p","12345","-s",\
                print (" ".join(cmd))
                p = subprocess.Popen(cmd,stdout=subprocess.PIPE)
                out = p.communicate()
                assert p.returncode == 0,"Error raxml"+out[0]
        except: pass # no need to worry about extra intermediate files
        return tree

It runs and returns the following code:

"raxml_wrapper.py", line 30, in raxml
        assert p.returncode == 0,"Error raxml"+out[0]
TypeError: Can't convert 'bytes' object to str implicitly

Initially, I tried the following:

 p = subprocess.Popen(cmd,stdout=subprocess.PIPE)
 p = p.decode('utf-8')
 out = p.communicate()
 assert p.returncode == 0,"Error raxml"+out[0]

That didn't fix the issue at all. I have looked at similar questions, but I cannot come up with a solution to this. I would appreciate some help on this.


Answer 1

p, a Popen object, doesn't have a .decode(...) member.

You need to actually decode the output

p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
out, _ = p.communicate()
out = out.decode('utf-8')
assert p.returncode == 0, 'Error raxml' + out[0]

That said, this code can be improved to use subprocess.check_output:

# does roughly the same thing, you'll get `subprocess.CalledProcessError` instead of `AssertionError`
out = subprocess.check_output(cmd).decode('UTF-8')

Or if you happen to be using python3.6+

out = subprocess.check_output(cmd, encoding='UTF-8')
Answer 2

I do not know exactly what your p.communicate() method does, but it seems that it returns a byte object as a result. And this piece of code, cannot add this byte object to "Error raxml" str object:

assert p.returncode == 0,"Error raxml"+out[0]

Maybe you should try converting it to str as this:

assert p.returncode == 0,"Error raxml"+str(out[0])
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