Update python #32
Update python #32
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yaoyuyang
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Update packages Update command for the storage engine Bump version numbers First pass migrating to python3 Pass flake8 tests Fix travis-ci
yaoyuyang
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| make_required_dirs(dbname) | ||
| cmd = "%s/makeblastdb -in %s -out %s " % (settings.NCBI_BIN_DIR, fafile, dbname) | ||
| cmd += "-title edge -dbtype nucl -parse_seqids -input_type fasta" | ||
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| r = subprocess.check_output(cmd.split(' ')) | ||
| if 'Adding sequences from FASTA' not in r: | ||
| print r | ||
| if b'Adding sequences from FASTA' not in r: |
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Why adding b here? @jamieleecho
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I get it. subprocess.check_output return its output as a byte string so we have to add an explicit b here otherwise it will throw error a bytes-like object is required, not 'str'
| @@ -20,7 +20,7 @@ def setUp(self): | |||
| Genome_Fragment(genome=self.genome, fragment=self.fragment, inherited=False).save() | |||
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| def test_outputs_fasta(self): | |||
| with tempfile.NamedTemporaryFile(mode='rw+', delete=False) as f: | |||
| with tempfile.NamedTemporaryFile(mode='w+', delete=False) as f: | |||
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What is the reason for removing r here? I'm sure it's valid python3 update, just wondering the reason.
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OK. I looked at python documents. w+ means writing and reading, therefore there is no need to add the r here.
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Got it. Tried rw+ and got the error must have exactly one of create/read/write/append mode so we have to use w+. I guess py3 is more strict about the file mode parameter than py2.
| @@ -13,8 +13,8 @@ def make_required_dirs(path): | |||
| dirn = os.path.dirname(path) | |||
| try: | |||
| original_umask = os.umask(0) | |||
| os.makedirs(dirn, 0777) | |||
| except: | |||
| os.makedirs(dirn, 0o777) | |||
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Got it. Octal number "0777" needs to be converted to new Python 3 friendly syntax: "0o777
This PR does the following:
Requires: #31