Correct bugs in export diversity

scripts/export_diversity.py

@@ -10,7 +10,7 @@ import sys
 import shutil
 
 # The input directory is the output of the Qiime2 diversity analysis
-INDIR = sys.argv[1]
+INDIR = sys.argv[1] if sys.argv[1].endswith("/") else sys.argv[1] + "/"
 OUTDIR = INDIR + "/tables/"
 
 ##################
@@ -26,7 +26,7 @@ for beta_diversity_metric in beta_diversity_metrics:
     artifact.export_data(OUTDIR + beta_diversity_metric.split("_distance_matrix")[0])
 
 # Move files to the output directory
-for sub_dir in os.listdir(OUTDIR):
+for sub_dir in [sub_dir for sub_dir in os.listdir(OUTDIR) if os.path.isdir(sub_dir)]:
     os.rename(OUTDIR + sub_dir + "/distance-matrix.tsv", OUTDIR + sub_dir + ".tsv")
     os.rmdir(OUTDIR + sub_dir)
 
@@ -68,4 +68,4 @@ artifact.export_data(OUTDIR)
 os.rename(OUTDIR + "feature-table.biom", OUTDIR + "rarefied_table.biom")
 
 # Convert BIOM to TSV
-os.system("biom convert -i " +  OUTDIR + "rarefied_table.biom -o " + OUTDIR + "rarefied_table.tsv  --to-tsv")
+os.system("biom convert -i " + OUTDIR + "rarefied_table.biom -o " + OUTDIR + "rarefied_table.tsv  --to-tsv")