annotate vpolo_convert.py @ 7:ff78e9c7b0d8 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
author bgruening
date Sat, 03 Oct 2020 18:21:49 +0000
parents e53f19161c59
children e4c01dcece8b
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e53f19161c59 "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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ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
bgruening
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2 import argparse
ff78e9c7b0d8 "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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e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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e53f19161c59 "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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ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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8 parser = argparse.ArgumentParser()
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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9 parser.add_argument("--mtx", "-m", action="store_true", help="--dumpMtx flag set")
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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10 parser.add_argument("--umi", "-u", action="store_true", help="--dumpUmiGraph flag set")
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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11 args = parser.parse_args()
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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13 if args.mtx:
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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14 alevin_df = par.read_quants_bin("output")
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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15 with open("quants_mat.tsv", "w") as f:
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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16 f.write(alevin_df.to_csv(sep="\t"))
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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18 if args.umi:
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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19 os.mkdir("umiout")
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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20 par.read_umi_graph("output", "umiout")