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[MRG] make sourmash compatible with khmer 3 #508

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Jun 27, 2018
Merged

[MRG] make sourmash compatible with khmer 3 #508

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2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@
language="c++",
extra_compile_args=EXTRA_COMPILE_ARGS,
extra_link_args=EXTRA_LINK_ARGS)],
"install_requires": ["screed>=0.9", "ijson", "khmer>=2.1<3.0"],
"install_requires": ["screed>=0.9", "ijson", "khmer>=2.1"],
"setup_requires": ['Cython>=0.25.2', "setuptools>=38.6.0"],
"extras_require": {
'test' : ['pytest', 'pytest-cov', 'numpy', 'matplotlib', 'scipy','recommonmark'],
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9 changes: 7 additions & 2 deletions sourmash/sbt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,11 @@ def search_transcript(node, seq, threshold):

import khmer

try:
load_nodegraph = khmer.load_nodegraph
except AttributeError:
load_nodegraph = khmer.Nodegraph.load

from .sbt_storage import FSStorage, TarStorage, IPFSStorage, RedisStorage
from .logging import error, notify, debug

Expand Down Expand Up @@ -785,7 +790,7 @@ def data(self):
with NamedTemporaryFile(suffix=".gz") as f:
f.write(data)
f.file.flush()
self._data = khmer.load_nodegraph(f.name)
self._data = load_nodegraph(f.name)
return self._data

@data.setter
Expand Down Expand Up @@ -838,7 +843,7 @@ def data(self):
with NamedTemporaryFile(suffix=".gz") as f:
f.write(data)
f.file.flush()
self._data = khmer.load_nodegraph(f.name)
self._data = load_nodegraph(f.name)
return self._data

@data.setter
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