comparison vpolo_convert.py @ 2:178ebdfe5a7e draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
author bgruening
date Tue, 15 Oct 2019 12:01:50 -0400
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children cfb0849582e1
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1:992c077f6e41 2:178ebdfe5a7e
1 #!/usr/bin/env python
2
3 from vpolo.alevin import parser as par
4 import argparse
5 import os
6
7 parser = argparse.ArgumentParser()
8 parser.add_argument("--mtx", "-m", action="store_true", help="--dumpMtx flag set")
9 parser.add_argument("--umi", "-u", action="store_true", help="--dumpUmiGraph flag set")
10 args = parser.parse_args()
11
12 if args.mtx:
13 alevin_df = par.read_quants_bin("output")
14 with open("quants_mat.tsv", "w") as f:
15 f.write(alevin_df.to_csv(sep="\t"))
16
17 if args.umi:
18 os.mkdir("umiout")
19 par.read_umi_graph("output", "umiout")