Mercurial > repos > bgruening > salmon
view vpolo_convert.py @ 15:cc05793bb896 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
author | bgruening |
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date | Sat, 03 Oct 2020 18:22:45 +0000 |
parents | 7fdb9d1591e2 |
children | 49121db48873 |
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#!/usr/bin/env python import argparse import os from vpolo.alevin import parser as par 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")