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Loads tree in NewickFormat, uses BP to parse tree faster #42

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merged 9 commits into from
Apr 4, 2021
Merged

Loads tree in NewickFormat, uses BP to parse tree faster #42

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e7d5708
uses BP to parse tree faster
ahdilmore Mar 18, 2021
d6213e5
Merge pull request #1 from ahdilmore/add-newick-format
ahdilmore Mar 18, 2021
12fded9
Moved get_bp code here
ahdilmore Mar 18, 2021
c490a0a
add bp import and work into phylo rpca command
cameronmartino Apr 1, 2021
dc4d400
fix bp input for CTF
cameronmartino Apr 1, 2021
b7d114f
extend bp import to standalone text
cameronmartino Apr 1, 2021
68399e7
fix imports in ctf/rclr
cameronmartino Apr 1, 2021
67aeab8
fix flake8
cameronmartino Apr 1, 2021
8b82c67
remove out of place comment
cameronmartino Apr 3, 2021
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10 changes: 9 additions & 1 deletion gemelli/rpca.py
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Expand Up @@ -19,10 +19,13 @@
DEFAULT_OPTSPACE_ITERATIONS,
DEFAULT_MFF)
from scipy.linalg import svd
from q2_types.tree import NewickFormat
from bp import parse_newick, to_skbio_treenode
from empress._plot_utils import get_bp


def phylogenetic_rpca(table: biom.Table,
phylogeny: TreeNode,
phylogeny: NewickFormat,
n_components: Union[int, str] = DEFAULT_COMP,
min_sample_count: int = DEFAULT_MSC,
min_feature_count: int = DEFAULT_MFC,
Expand All @@ -39,6 +42,11 @@ def phylogenetic_rpca(table: biom.Table,
gemelli.
"""

# loads NewickFormat tree as bp.BP tree; loads & parses tree faster
phylogeny = get_bp(phylogeny)
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get_bp is only like two lines and it is pretty easy to get burned by importing from private modules in python. I would probably recommend just duplicating that code here.

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phylogeny = phylogeny.shear(set((table.ids('observation')).flatten()))
phylogeny = to_skbio_treenode(phylogeny)
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# use helper to process table
table = rpca_table_processing(table,
min_sample_count,
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3 changes: 2 additions & 1 deletion setup.py
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Expand Up @@ -108,7 +108,8 @@ def run(self):
'scikit-learn >= 0.18.1',
'scikit-bio > 0.5.3',
'biom-format',
'h5py', ],
'h5py',
'iow',],
classifiers=classifiers,
entry_points={'qiime2.plugins': q2cmds,
'console_scripts': standalone},
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