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Merged
merged 3 commits into from
Apr 7, 2021
Merged

v2021.2 #12

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a0d7f85
updated for latest version
gavinmdouglas Mar 18, 2021
be2d244
added edge exponent and placement tool options
gavinmdouglas Apr 6, 2021
15d3fe6
removed outdated processes option
gavinmdouglas Apr 7, 2021
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10 changes: 7 additions & 3 deletions q2_picrust2/_custom_tree_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ def custom_tree_pipeline(table: biom.Table,
threads: int = 1,
hsp_method: str = "mp",
max_nsti: float = 2.0,
edge_exponent: float = 0.5,
skip_minpath: bool = False,
no_gap_fill: bool = False,
skip_norm: bool = False,
Expand Down Expand Up @@ -45,23 +46,26 @@ def custom_tree_pipeline(table: biom.Table,
" -p 1 " + \
" -n " + \
" -o " + hsp_out_16S + \
" -m " + hsp_method
" -m " + hsp_method + \
" -e " + str(edge_exponent)

hsp_out_EC = path.join(picrust2_out, "EC_predicted.tsv.gz")
hsp_out_EC_cmd = "hsp.py -i EC " + \
" -t " + newick_infile + \
" -p " + str(threads) + \
" -n " + \
" -o " + hsp_out_EC + \
" -m " + hsp_method
" -m " + hsp_method + \
" -e " + str(edge_exponent)

hsp_out_KO = path.join(picrust2_out, "KO_predicted.tsv.gz")
hsp_out_KO_cmd = "hsp.py -i KO " + \
" -t " + newick_infile + \
" -p " + str(threads) + \
" -n " + \
" -o " + hsp_out_KO + \
" -m " + hsp_method
" -m " + hsp_method + \
" -e " + str(edge_exponent)

if highly_verbose:
hsp_out_16S_cmd += " --verbose"
Expand Down
4 changes: 4 additions & 0 deletions q2_picrust2/_full_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,10 @@ def full_pipeline(table: biom.Table,
seq: pd.Series,
threads: int = 1,
hsp_method: str = "mp",
placement_tool: str = "epa-ng",
min_align: float = 0.8,
max_nsti: float = 2.0,
edge_exponent: float = 0.5,
skip_minpath: bool = False,
no_gap_fill: bool = False,
skip_norm: bool = False,
Expand Down Expand Up @@ -44,6 +46,7 @@ def full_pipeline(table: biom.Table,
input_table=biom_infile,
output_folder=picrust2_out,
processes=threads,
placement_tool=placement_tool,
ref_dir=default_ref_dir,
in_traits="EC,KO",
custom_trait_tables=None,
Expand All @@ -58,6 +61,7 @@ def full_pipeline(table: biom.Table,
min_reads=1,
min_samples=1,
hsp_method=hsp_method,
edge_exponent=edge_exponent,
min_align=min_align,
skip_nsti=False,
skip_minpath=skip_minpath,
Expand Down
13 changes: 8 additions & 5 deletions q2_picrust2/citations.bib
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Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
@article{Douglas2019bioRxiv,
title={PICRUSt2: An improved and extensible approach for metagenome inference},
@article{Douglas2020NatureBiotech,
title={PICRUSt2 for prediction of metagenome functions},
author={Douglas et al.},
journal={bioRxiv},
year={2019},
doi={10.1101/672295}
journal={Nature Biotechnology},
year={2020},
volume={38},
issue={6},
pages={685-688},
doi={10.1038/s41587-020-0548-6}
}

26 changes: 22 additions & 4 deletions q2_picrust2/plugin_setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,16 +9,18 @@

HSP_METHODS = ['mp', 'emp_prob', 'pic', 'scp', 'subtree_average']

PLACEMENT_TOOLS = ['epa-ng', 'sepp']

plugin = Plugin(
name='picrust2',
version="2019.10",
version="2021.2",
website='https://github.com/gavinmdouglas/q2-picrust2',
package='q2_picrust2',
description=('This QIIME 2 plugin wraps the default 16S PICRUSt2 pipeline to run '
'metagenome inference based on marker gene data. Currently '
'only unstratified output is supported.'),
short_description='Predicts gene families and pathways from 16S sequences.',
citations=[citations['Douglas2019bioRxiv']]
citations=[citations['Douglas2020NatureBiotech']]
)

plugin.methods.register_function(
Expand All @@ -29,8 +31,10 @@

parameters={'threads': Int % Range(1, None),
'hsp_method': Str % Choices(HSP_METHODS),
'placement_tool': Str % Choices(PLACEMENT_TOOLS),
'min_align': Float % Range(0.0, 1.0),
'max_nsti': Float % Range(0.0, None),
'edge_exponent': Float % Range(0.0, None),
'skip_minpath': Bool,
'no_gap_fill': Bool,
'skip_norm': Bool,
Expand All @@ -49,6 +53,9 @@
parameter_descriptions={
'threads': 'Number of threads/processes to use during workflow.',
'hsp_method': 'Which hidden-state prediction method to use.',
'placement_tool': ('Placement tool to use when placing sequences into '
'reference tree. EPA-ng is the default, but SEPP '
'is less memory intensive.'),
'min_align': ('Proportion of the total length of an input query '
'sequence that must align with reference sequences. '
'Any sequences with lengths below this value after '
Expand All @@ -59,6 +66,11 @@
'be output.'),
'skip_minpath': ('Do not run MinPath to identify which pathways are '
'present as a first pass (on by default).'),
'edge_exponent': ('Setting for maximum parisomony hidden-state '
'prediction. Specifies weighting transition costs '
'by the inverse length of edge lengths. If 0, then '
'edge lengths do not influence predictions. Must be '
'a non-negative real-valued number.'),
'no_gap_fill': ('Do not perform gap filling before predicting '
'pathway abundances (gap filling is on otherwise by '
'default).'),
Expand All @@ -83,7 +95,7 @@

description=("QIIME 2 plugin for default 16S PICRUSt2 pipeline"),

citations=[citations['Douglas2019bioRxiv']]
citations=[citations['Douglas2020NatureBiotech']]
)


Expand All @@ -96,6 +108,7 @@
parameters={'threads': Int % Range(1, None),
'hsp_method': Str % Choices(HSP_METHODS),
'max_nsti': Float % Range(0.0, None),
'edge_exponent': Float % Range(0.0, None),
'skip_minpath': Bool,
'no_gap_fill': Bool,
'skip_norm': Bool,
Expand All @@ -119,6 +132,11 @@
'be output.'),
'skip_minpath': ('Do not run MinPath to identify which pathways are '
'present as a first pass (on by default).'),
'edge_exponent': ('Setting for maximum parisomony hidden-state '
'prediction. Specifies weighting transition costs '
'by the inverse length of edge lengths. If 0, then '
'edge lengths do not influence predictions. Must be '
'a non-negative real-valued number.'),
'no_gap_fill': ('Do not perform gap filling before predicting '
'pathway abundances (gap filling is on otherwise by '
'default).'),
Expand Down Expand Up @@ -146,5 +164,5 @@
"used with the output of SEPP (q2-fragment-insertion) as a " +
"starting point."),

citations=[citations['Douglas2019bioRxiv']]
citations=[citations['Douglas2020NatureBiotech']]
)
2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

setup(
name="q2-picrust2",
version="2019.10",
version="2021.2",
packages=find_packages(),
package_data={'q2_picrust2': ['citations.bib']},
author="Gavin Douglas",
Expand Down