diff vpolo_convert.py @ 2:178ebdfe5a7e draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vpolo_convert.py	Tue Oct 15 12:01:50 2019 -0400
@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+
+from vpolo.alevin import parser as par
+import argparse
+import os
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--mtx", "-m", action="store_true", help="--dumpMtx flag set")
+parser.add_argument("--umi", "-u", action="store_true", help="--dumpUmiGraph flag set")
+args = parser.parse_args()
+
+if args.mtx:
+    alevin_df = par.read_quants_bin("output")
+    with open("quants_mat.tsv", "w") as f:
+        f.write(alevin_df.to_csv(sep="\t"))
+
+if args.umi:
+    os.mkdir("umiout")
+    par.read_umi_graph("output", "umiout")