Merge pull request #663 from anupriyatripathi/remove-itol

Debug empress integration
CCMS-UCSD · Dec 23, 2020 · ace95d8 · ace95d8
2 parents ccc7197 + 56f240c
commit ace95d8
Showing 1 changed file with 21 additions and 8 deletions.
diff --git a/qemistree/tools/qemistree/qemistree.py b/qemistree/tools/qemistree/qemistree.py
@@ -43,6 +43,8 @@ def main():
     output_pcoa_qza = os.path.join(args.output_folder, "pcoa.qza")
     output_emperor_qza = os.path.join(args.output_folder, "emperor.qzv")
     output_qemistree_empress_qzv = os.path.join(args.output_folder, "qemistree-empress.qzv")
+    input_metadata_folder = args.input_metadata_folder
+    output_sample_metadata = os.path.join(args.output_folder, "qiime2_metadata.tsv")
 
     all_cmd = []
 
@@ -171,15 +173,26 @@ def main():
             output_emperor_qza)
         all_cmd.append(cmd)
 
-    # Tree Plotting
-    cmd = f'source {args.conda_activate_bin} {args.conda_environment} && LC_ALL=en_US.UTF-8 && export LC_ALL && qiime empress community-plot \
-    --i-feature-table {output_merged_feature_table_qza} \
-    --i-tree {output_qemistree_pruned_qza} \
-    --m-feature-metadata-file {output_classified_feature_data_qza} \
-    --m-sample-metadata-file {metadata_files[0]} \
-    --o-visualization {output_qemistree_empress_qzv}'
-    all_cmd.append(cmd)
+        # Tree Plotting
+        cmd = f'source {args.conda_activate_bin} {args.conda_environment} && LC_ALL=en_US.UTF-8 && export LC_ALL && qiime empress community-plot \
+        --i-feature-table {output_merged_feature_table_qza} \
+        --i-tree {output_qemistree_pruned_qza} \
+        --m-feature-metadata-file {output_classified_feature_data_qza} \
+        --m-sample-metadata-file {metadata_files[0]} \
+        --o-visualization {output_qemistree_empress_qzv}'
+        all_cmd.append(cmd)
 
+        # saving sample metadata
+        cmd = "cp {} {}".format(metadata_files[0], output_sample_metadata)
+        all_cmd.append(cmd)
+    else:
+        # Tree Plotting without sample metadata
+        cmd = f'source {args.conda_activate_bin} {args.conda_environment} && LC_ALL=en_US.UTF-8 && export LC_ALL && qiime empress tree-plot \
+        --i-tree {output_qemistree_pruned_qza} \
+        --m-feature-metadata-file {output_classified_feature_data_qza} \
+        --o-visualization {output_qemistree_empress_qzv}'
+        all_cmd.append(cmd)
+
     #Actually running all the commands
     output_command_log_filename = os.path.join(args.output_folder, "run_log.txt")
     with open(output_command_log_filename, "w") as log_file: