Merge pull request #153 from sfiligoi/h5unifrac_multi

Add h5unifrac_all method

Author: sfiligoi

.github/workflows/main.yml

@@ -114,6 +114,13 @@ jobs:
         python -c "import h5py,skbio; dm = skbio.DistanceMatrix.read('ci/test.dm'); f_u=h5py.File('ci/test2.dm.h5','r'); dm_u=skbio.stats.distance.DistanceMatrix(f_u['matrix'][:,:],f_u['order'][:]); t=abs(dm_u.data-dm.data).max(); print(t); assert t < 0.1"
         python -c "import h5py; f_u=h5py.File('ci/test2.dm.h5','r'); print(f_u.keys()); assert len(f_u['stat_methods'][:]) == 1"
         python -c "import h5py; f_u=h5py.File('ci/test3.dm.h5','r'); print(f_u.keys()); assert len(f_u['pcoa_eigvals'][:]) == 2"
+        # repeat using unifrac's h5 interfaces
+        python -c "import unifrac; dm_u=unifrac.h5unifrac('ci/test.dm.h5'); dm_l=unifrac.h5unifrac_all('ci/test.dm.h5')"
+        python -c "import unifrac,skbio; dm = skbio.DistanceMatrix.read('ci/test.dm'); dm_u=unifrac.h5unifrac('ci/test.dm.h5'); t=abs(dm_u.data-dm.data).max(); print(t); assert t < 0.1"
+        python -c "import unifrac,skbio; dm = skbio.DistanceMatrix.read('ci/test.dm'); dm_u=unifrac.h5unifrac_all('ci/test.dm.h5')[0]; t=abs(dm_u.data-dm.data).max(); print(t); assert t < 0.1"
+        python -c "import unifrac,skbio; dm = skbio.DistanceMatrix.read('ci/test.dm'); dm_u=unifrac.h5unifrac('ci/test2.dm.h5'); t=abs(dm_u.data-dm.data).max(); print(t); assert t < 0.1"
+        python -c "import unifrac; st_l=unifrac.h5permanova_dict('ci/test2.dm.h5'); assert len(st_l) == 1"
+        python -c "import unifrac; pc=unifrac.h5pcoa('ci/test3.dm.h5'); print(pc); assert len(pc.eigvals) == 2"
         if [[ "$(uname -s)" == "Linux" ]]; 
         then
           MD5=md5sum

README.md

@@ -140,13 +140,14 @@ The library can be accessed directly from within Python. If operating in this mo
     >>> import unifrac
     >>> dir(unifrac)
     ['__all__', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__',
-     '__package__', '__path__', '__spec__', '__version__', '_api', '_meta', '_methods', 'set_random_seed', 'faith_pd',
-     'generalized', 'generalized_fp32', 'generalized_fp32_to_file', 'generalized_fp64', 'generalized_fp64_to_file', 'generalized_to_file',
-     'h5pcoa', 'h5pcoa_all', 'h5permanova', 'h5permanova_dict', 'h5unifrac', 'meta', 'pkg_resources', 'ssu', 'ssu_fast', 'ssu_inmem', 'ssu_to_file', 'ssu_to_file_v2',
-     'unweighted', 'unweighted_fp32', 'unweighted_fp32_to_file', 'unweighted_fp64', 'unweighted_fp64_to_file', 'unweighted_to_file',
-     'weighted_normalized', 'weighted_normalized_fp32', 'weighted_normalized_fp32_to_file', 'weighted_normalized_fp64', 'weighted_normalized_fp64_to_file',
-     'weighted_normalized_to_file', 'weighted_unnormalized', 'weighted_unnormalized_fp32', 'weighted_unnormalized_fp32_to_file', 'weighted_unnormalized_fp64', 
-     'weighted_unnormalized_fp64_to_file', 'weighted_unnormalized_to_file']
+     '__package__', '__path__', '__spec__', '__version__', '_api', '_meta', '_methods',
+     'faith_pd', 'generalized', 'generalized_fp32', 'generalized_fp32_to_file', 'generalized_fp64', 'generalized_fp64_to_file', 'generalized_to_file',
+     'h5pcoa', 'h5pcoa_all', 'h5permanova', 'h5permanova_dict', 'h5unifrac', 'h5unifrac_all', 'meta', 'pkg_resources',
+     'set_random_seed', 'ssu', 'ssu_fast', 'ssu_inmem', 'ssu_to_file', 'ssu_to_file_v2', 'unweighted', 'unweighted_fp32',
+     'unweighted_fp32_to_file', 'unweighted_fp64', 'unweighted_fp64_to_file', 'unweighted_to_file', 'weighted_normalized',
+     'weighted_normalized_fp32', 'weighted_normalized_fp32_to_file', 'weighted_normalized_fp64', 'weighted_normalized_fp64_to_file',
+     'weighted_normalized_to_file', 'weighted_unnormalized', 'weighted_unnormalized_fp32', 'weighted_unnormalized_fp32_to_file', 
+     'weighted_unnormalized_fp64', 'weighted_unnormalized_fp64_to_file', 'weighted_unnormalized_to_file']
     >>> print(unifrac.unweighted.__doc__)
     Compute Unweighted UniFrac
 

unifrac/__init__.py

@@ -33,7 +33,7 @@
                               weighted_unnormalized_fp32_to_file,
                               generalized_fp32_to_file,
                               meta,
-                              h5unifrac,
+                              h5unifrac, h5unifrac_all,
                               h5pcoa, h5pcoa_all,
                               h5permanova, h5permanova_dict)
 from unifrac._api import ssu, ssu_fast, faith_pd, set_random_seed
@@ -57,7 +57,7 @@
            'weighted_normalized_fp32_to_file',
            'weighted_unnormalized_fp32_to_file',
            'generalized_fp32_to_file',
-           'h5unifrac', 'h5pcoa', 'h5pcoa_all',
+           'h5unifrac', 'h5unifrac_all', 'h5pcoa', 'h5pcoa_all',
            'h5permanova', 'h5permanova_dict',
            'ssu', 'ssu_fast', 'faith_pd',
            'ssu_to_file', 'ssu_to_file_v2',

unifrac/_methods.py

@@ -2508,7 +2508,7 @@ def generalized_fp32_to_file(table: str,
 
 
 def h5unifrac(h5file: str) -> skbio.DistanceMatrix:
-    """Read UniFrac from a hdf5 file
+    """Read UniFrac distance matrix from a hdf5 file
 
     Parameters
     ----------
@@ -2538,13 +2538,68 @@ def h5unifrac(h5file: str) -> skbio.DistanceMatrix:
     """
 
     with h5py.File(h5file, "r") as f_u:
-        dm = skbio.DistanceMatrix(
+        if 'matrix:0' in f_u.keys():
+            # multi format
+            dm = skbio.DistanceMatrix(
+               f_u['matrix:0'][:, :],
+               [c.decode('ascii') for c in f_u['order'][:]])
+        else:
+            # single format
+            dm = skbio.DistanceMatrix(
                f_u['matrix'][:, :],
                [c.decode('ascii') for c in f_u['order'][:]])
 
     return dm
 
 
+def h5unifrac_all(h5file: str) -> skbio.DistanceMatrix:
+    """Read all UniFrac distance matrices from a hdf5 file
+
+    Parameters
+    ----------
+    h5file : str
+        A filepath to a hdf5 file.
+
+    Returns
+    -------
+    tuple(skbio.DistanceMatrix)
+        The distance matrices.
+
+    Raises
+    ------
+    OSError
+        If the hdf5 file is not found
+    KeyError
+        If the hdf5 does not have the necessary fields
+
+    References
+    ----------
+    .. [1] Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for
+       comparing microbial communities. Appl. Environ. Microbiol. 71, 8228-8235
+       (2005).
+    .. [2] Chang, Q., Luan, Y. & Sun, F. Variance adjusted weighted UniFrac: a
+       powerful beta diversity measure for comparing communities based on
+       phylogeny. BMC Bioinformatics 12:118 (2011).
+    """
+
+    with h5py.File(h5file, "r") as f_u:
+        order = [c.decode('ascii') for c in f_u['order'][:]]
+        if 'matrix' in f_u.keys():
+            # single format
+            dms = [skbio.DistanceMatrix(
+               f_u['matrix'][:, :], order)]
+        else:
+            # multi format
+            dms = []
+            i = 0
+            while 'matrix:%i' % i in f_u.keys():
+                dms.append(skbio.DistanceMatrix(
+                             f_u['matrix:%i' % i][:, :], order))
+                i = i + 1
+
+    return dms
+
+
 def _build_pcoa(f_u, long_method_name, order_index,
                 eigval_key, samples_key, prop_key):
     axis_labels = ["PC%d" % i for i in
@@ -2597,9 +2652,16 @@ def h5pcoa(h5file: str) -> skbio.OrdinationResults:
         order_index = [c.decode('ascii')
                        for c in f_u['order'][:]]
 
-        pc = _build_pcoa(f_u, long_method_name, order_index,
-                         'pcoa_eigvals', 'pcoa_samples',
-                         'pcoa_proportion_explained')
+        if 'pcoa_eigvals:0' in f_u.keys():
+            # multi interface
+            pc = _build_pcoa(f_u, long_method_name, order_index,
+                             'pcoa_eigvals:0', 'pcoa_samples:0',
+                             'pcoa_proportion_explained:0')
+        else:
+            # single interface
+            pc = _build_pcoa(f_u, long_method_name, order_index,
+                             'pcoa_eigvals', 'pcoa_samples',
+                             'pcoa_proportion_explained')
 
     return pc