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annotate vpolo_convert.py @ 9:58b9ef13fcca draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888
author bgruening
date Wed, 29 Oct 2025 10:45:39 +0000
parents 510af1a0f9c8
children
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7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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1 #!/usr/bin/env python
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bgruening
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2 import argparse
28e01a2960a5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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3 import os
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7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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5 from vpolo.alevin import parser as par
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28e01a2960a5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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7 parser = argparse.ArgumentParser()
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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8 parser.add_argument("--mtx", "-m", action="store_true", help="--dumpMtx flag set")
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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9 parser.add_argument("--umi", "-u", action="store_true", help="--dumpUmiGraph flag set")
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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10 args = parser.parse_args()
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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12 if args.mtx:
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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13 alevin_df = par.read_quants_bin("output")
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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14 with open("quants_mat.tsv", "w") as f:
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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15 f.write(alevin_df.to_csv(sep="\t"))
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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17 if args.umi:
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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18 os.mkdir("umiout")
7c618ec039b8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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19 par.read_umi_graph("output", "umiout")