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Merge pull request #14 from pinellolab/dev
Add editing preference profiling
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| import argparse | ||
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| def parse_args(): | ||
| print(" \n~~~BEAN Profile~~~") | ||
| print("-Profile editing patterns of your editor-") | ||
| print( | ||
| r""" | ||
| _ _ __ _ _ | ||
| / \ '\ _ __ _ _ ___ / _(_) |___ | ||
| | \ \ | '_ \ '_/ _ \ _| | / -_) | ||
| \ \ | | .__/_| \___/_| |_|_\___| | ||
| `.__|/ |_| | ||
| """ | ||
| ) | ||
| parser = argparse.ArgumentParser() | ||
| parser.add_argument( | ||
| "bdata_path", help="Path to the ReporterScreen object to run QC on", type=str | ||
| ) | ||
| parser.add_argument( | ||
| "-o", | ||
| "--output-prefix", | ||
| help="Output prefix of editing pattern report (prefix.html, prefix.ipynb). If not provided, base name of `bdata_path` is used.", | ||
| type=str, | ||
| ) | ||
| parser.add_argument( | ||
| "--replicate-col", | ||
| help="Column name in `bdata.samples` that describes replicate ID.", | ||
| type=str, | ||
| default="rep", | ||
| ) | ||
| parser.add_argument( | ||
| "--condition-col", | ||
| help="Column name in `bdata.samples` that describes experimental condition. (sorting bin, time, etc.)", | ||
| type=str, | ||
| default="bin", | ||
| ) | ||
| parser.add_argument( | ||
| "--pam-col", | ||
| help="Column name describing PAM of each gRNA in `bdata.guides`.", | ||
| type=str, | ||
| default=None, | ||
| ) | ||
| parser.add_argument( | ||
| "--control-condition", | ||
| help="Control condition where editing preference would be profiled at. Pre-filters data where `bdata.samples[condition_col] == control_condition`.", | ||
| type=str, | ||
| default="bulk", | ||
| ) | ||
| parser.add_argument( | ||
| "-w", | ||
| "--window-length", | ||
| help="Window length of editing window of maximal editing efficiency to be identified. This window is used to quantify context specificity within the window.", | ||
| type=int, | ||
| default=6, | ||
| ) | ||
|
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| args = parser.parse_args() | ||
| if args.output_prefix is None: | ||
| args.output_prefix = f"{args.bdata_path.rsplit('.h5ad', 1)[0]}" | ||
| return args | ||
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| def check_args(args): | ||
| if args.window_length < 1: | ||
| raise ValueError(f"window_length {args.window_length} is too small.") | ||
| if args.window_length > 20: | ||
| raise ValueError(f"window_length {args.window_length} is too large.") | ||
| return args |
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