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Merged
merged 3 commits into from
May 20, 2019
Merged

V2.1.4 b update #8

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e27376d
updated to match latest PICRUSt2 version
gavinmdouglas May 20, 2019
c1bf377
added to gitignore
gavinmdouglas May 20, 2019
e6a34cd
changed version number to qiime2 release number
gavinmdouglas May 20, 2019
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1 +1,3 @@
testfiles/*
q2_picrust2.egg-info/
q2_picrust2/__pycache__/
37 changes: 22 additions & 15 deletions q2_picrust2/_custom_tree_pipeline.py
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Expand Up @@ -2,6 +2,7 @@
import skbio
import biom
from os import path
import sys
import pandas as pd
from tempfile import TemporaryDirectory
from q2_types.feature_table import FeatureTable, Frequency
Expand Down Expand Up @@ -31,59 +32,65 @@ def custom_tree_pipeline(table: biom.Table,

picrust2_out = path.join(temp_dir, "picrust2_out")

print("Running the below commands:", file=sys.stderr)

# Run hidden-state prediction step (on 16S, EC, and KO tables
# separately.
hsp_out_16S = path.join(picrust2_out, "16S_predicted.tsv")
hsp_out_16S = path.join(picrust2_out, "16S_predicted.tsv.gz")
system_call_check("hsp.py -i 16S " +
" -t " + newick_infile +
" -p 1 " +
" -n " +
"-o " + hsp_out_16S +
" -m " + hsp_method)
" -m " + hsp_method,
print_out=True)

hsp_out_EC = path.join(picrust2_out, "EC_predicted.tsv")
hsp_out_EC = path.join(picrust2_out, "EC_predicted.tsv.gz")
system_call_check("hsp.py -i EC " +
" -t " + newick_infile +
" -p " + str(threads) +
" -o " + hsp_out_EC +
" -m " + hsp_method)
" -m " + hsp_method,
print_out=True)

hsp_out_KO = path.join(picrust2_out, "KO_predicted.tsv")
hsp_out_KO = path.join(picrust2_out, "KO_predicted.tsv.gz")
system_call_check("hsp.py -i KO " +
" -t " + newick_infile +
" -p " + str(threads) +
" -o " + hsp_out_KO +
" -m " + hsp_method)
" -m " + hsp_method,
print_out=True)

# Run metagenome pipeline step.
EC_metagenome_out = path.join(picrust2_out, "EC_metagenome_out")
system_call_check("metagenome_pipeline.py -i " + biom_infile +
" -m " + hsp_out_16S +
" -f " + hsp_out_EC +
" -o " + EC_metagenome_out +
" --max_nsti " + str(max_nsti))
" --max_nsti " + str(max_nsti),
print_out=True)

KO_metagenome_out = path.join(picrust2_out, "KO_metagenome_out")
system_call_check("metagenome_pipeline.py -i " + biom_infile +
" -m " + hsp_out_16S +
" -f " + hsp_out_KO +
" -o " + KO_metagenome_out +
" --max_nsti " + str(max_nsti))
" --max_nsti " + str(max_nsti),
print_out=True)

EC_out = path.join(EC_metagenome_out, "pred_metagenome_unstrat.tsv.gz")
KO_out = path.join(KO_metagenome_out, "pred_metagenome_unstrat.tsv.gz")

# Run pathway inference step.
pathways_out = path.join(picrust2_out, "pathways_out")

EC_out = path.join(EC_metagenome_out, "pred_metagenome_unstrat.tsv")

pathabun_out = path.join(pathways_out, "path_abun_unstrat.tsv.gz")
system_call_check("pathway_pipeline.py -i " + EC_out +
" -o " + pathways_out +
" -p " + str(threads))
" -p " + str(threads),
print_out=True)

# Read in output unstratified metagenome tables and return as BIOM
# objects.
KO_out = path.join(KO_metagenome_out, "pred_metagenome_unstrat.tsv")
pathabun_out = path.join(pathways_out, "path_abun_unstrat.tsv")

ko_biom = biom.load_table(KO_out)
ec_biom = biom.load_table(EC_out)
pathabun_biom = biom.load_table(pathabun_out)
Expand Down
5 changes: 4 additions & 1 deletion q2_picrust2/_full_pipeline.py
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Expand Up @@ -40,15 +40,17 @@ def full_pipeline(table: biom.Table,
func_outputs, pathway_outputs = picrust2.pipeline.full_pipeline(study_fasta=seq_outfile,
input_table=biom_infile,
output_folder=picrust2_out,
threads=threads,
processes=threads,
ref_dir=default_ref_dir,
in_traits="EC,KO",
custom_trait_tables=None,
marker_gene_table=default_tables["16S"],
pathway_map=default_pathway_map,
rxn_func="EC",
no_pathways=False,
regroup_map=default_regroup_map,
no_regroup=False,
metagenome_contrib=True,
stratified=False,
max_nsti=max_nsti,
min_reads=1,
Expand All @@ -59,6 +61,7 @@ def full_pipeline(table: biom.Table,
skip_minpath=False,
coverage=False,
per_sequence_contrib=False,
remove_intermediate=False,
verbose=True)

# Convert the returned unstratified tables to BIOM tables.
Expand Down
2 changes: 1 addition & 1 deletion q2_picrust2/plugin_setup.py
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Expand Up @@ -13,7 +13,7 @@

plugin = Plugin(
name='picrust2',
version="0.0.3",
version="2019.4",
website='https://github.com/gavinmdouglas/q2-picrust2',
package='q2_picrust2',
description=('This QIIME 2 plugin wraps the default 16S PICRUSt2 pipeline to run '
Expand Down
2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -2,7 +2,7 @@

setup(
name="q2-picrust2",
version="0.0.3",
version="2019.4",
packages=find_packages(),
package_data={'q2_picrust2': ['citations.bib']},
author="Gavin Douglas",
Expand Down