moved resources to package folder

krol33 · Oct 11, 2016 · 7515e88 · 7515e88
1 parent 115f255
commit 7515e88
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Showing 8 changed files with 11 additions and 5 deletions.
diff --git a/abruijn/polish.py b/abruijn/polish.py
@@ -27,6 +27,9 @@
 class PolishException(Exception):
     pass
 
+def get_root():
+    return os.path.dirname(__file__)
+
 
 def check_binaries():
     if not which(POLISH_BIN):
@@ -42,10 +45,12 @@ def check_binaries():
 
 def polish(bubbles, num_proc, err_mode, work_dir, iter_id):
     logger.info("Correcting bubbles")
+
+    _ROOT = get_root()
 
-    subs_matrix = os.path.join(os.environ["ABRUIJN_RES"],
+    subs_matrix = os.path.join(_ROOT, 'resource',
                                config.vals["err_modes"][err_mode]["subs_matrix"])
-    hopo_matrix = os.path.join(os.environ["ABRUIJN_RES"],
+    hopo_matrix = os.path.join(_ROOT, 'resource',
                                config.vals["err_modes"][err_mode]["hopo_matrix"])
 
     bubbles_file = os.path.join(work_dir, "bubbles_{0}.fasta".format(iter_id))

diff --git a/resource/nano_homopolymers.mat → abruijn/resource/nano_homopolymers.mat b/resource/nano_homopolymers.mat → abruijn/resource/nano_homopolymers.mat
diff --git a/resource/nano_substitutions.mat → abruijn/resource/nano_substitutions.mat b/resource/nano_substitutions.mat → abruijn/resource/nano_substitutions.mat
diff --git a/resource/p6c4_homopolymers.mat → abruijn/resource/p6c4_homopolymers.mat b/resource/p6c4_homopolymers.mat → abruijn/resource/p6c4_homopolymers.mat
diff --git a/resource/p6c4_substitutions.mat → abruijn/resource/p6c4_substitutions.mat b/resource/p6c4_substitutions.mat → abruijn/resource/p6c4_substitutions.mat
diff --git a/resource/pacbio_homopolymers.mat → abruijn/resource/pacbio_homopolymers.mat b/resource/pacbio_homopolymers.mat → abruijn/resource/pacbio_homopolymers.mat
diff --git a/resource/pacbio_substitutions.mat → abruijn/resource/pacbio_substitutions.mat b/resource/pacbio_substitutions.mat → abruijn/resource/pacbio_substitutions.mat
diff --git a/setup.py b/setup.py
@@ -10,9 +10,10 @@
       author='Mikhail Kolmogorov',
       author_email = '',
       license='BSD-3-Clause',
-      packages=find_packages(),
+      packages=['abruijn'],
+      package_data={'abruijn': ['resource/*.mat']},
       scripts = ['bin/abruijn-assemble', 'bin/abruijn-polish', 'scripts/abruijn'],
-      data_files=['resource/nano_homopolymers.mat', 'resource/nano_substitutions.mat', 'resource/p6c4_homopolymers.mat',
-                  'resource/p6c4_substitutions.mat', 'resource/pacbio_homopolymers.mat', 'resource/pacbio_substitutions.mat']
+      #data_files=['resource/nano_homopolymers.mat', 'resource/nano_substitutions.mat', 'resource/p6c4_homopolymers.mat',
+      #            'resource/p6c4_substitutions.mat', 'resource/pacbio_homopolymers.mat', 'resource/pacbio_substitutions.mat']
       )