Merge pull request #8 from gavinmdouglas/v2.1.4-b_update

V2.1.4 b update

Author: gavinmdouglas

.gitignore

@@ -1 +1,3 @@
 testfiles/*
+q2_picrust2.egg-info/
+q2_picrust2/__pycache__/

q2_picrust2/_custom_tree_pipeline.py

@@ -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
@@ -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)

q2_picrust2/_full_pipeline.py

@@ -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,
@@ -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.

q2_picrust2/plugin_setup.py

@@ -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 '

setup.py

@@ -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",