Commit d36aa5c5 authored by Erwan DELAGE's avatar Erwan DELAGE
Browse files

Use os rather than subprocess to export rarefied table, bug cluster

parent 6d568a03
......@@ -8,7 +8,6 @@ import pandas as pd
import os
import sys
import shutil
import subprocess
# The input directory is the output of the Qiime2 diversity analysis
INDIR = sys.argv[1]
......@@ -69,6 +68,4 @@ artifact.export_data(OUTDIR)
os.rename(OUTDIR + "feature-table.biom", OUTDIR + "rarefied_table.biom")
# Convert BIOM to TSV
process = subprocess.Popen(['biom', 'convert', '-i', OUTDIR + "rarefied_table.biom", '-o', OUTDIR + "rarefied_table.tsv", "--to-tsv"],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
os.system("biom convert -i " + OUTDIR + "rarefied_table.biom -o " + OUTDIR + "rarefied_table.tsv --to-tsv")
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment