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import-rna: Treat --max-log2 as float, so it's usable
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Previously the default +3.0 worked, but user-specifed values were
treated as strings and did not work.
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etal committed Oct 4, 2018
1 parent ef30d39 commit 6e6e85b
Showing 1 changed file with 3 additions and 2 deletions.
5 changes: 3 additions & 2 deletions cnvlib/commands.py
Original file line number Diff line number Diff line change
Expand Up @@ -1488,9 +1488,10 @@ def _cmd_import_rna(args):
P_import_rna.add_argument('-c', '--correlations', metavar="FILE",
help="""Correlation of each gene's copy number with
expression. Output of cnv_expression_correlate.py.""")
P_import_rna.add_argument('--max-log2', metavar="FLOAT", default=3.0,
P_import_rna.add_argument('--max-log2',
metavar="FLOAT", default=3.0, type=float,
help="""Maximum log2 value in output. Observed values above this limit
will be replaced with this value.""")
will be replaced with this value. [Default: %(default)s]""")
P_import_rna.add_argument('-n', '--normal', nargs='+', default=[],
help="""Normal samples (same format as `gene_counts`) to be used as a
control to when normalizing and re-centering gene read depth
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