enhance operations

utils/nanomethphaseMethylFreq2methylkit.py

@@ -0,0 +1,52 @@
+#!/usr/bin/env python3
+"""
+Input is start 0-base, end 1-base, from Nanomethphase phased results meth freq tsv file (with or without header)
+Output is base 1-base, used for methylkit input
+
+Note: methylkit prefer 1-based input, since the output DMC will be correct, default input tsv is no header
+"""
+
+import argparse
+
+import pandas as pd
+
+from nanome.common.global_config import logger, set_log_debug_level, set_log_info_level
+
+
+def parse_arguments():
+    parser = argparse.ArgumentParser(prog='Convert nanomethphase MethylFreq to methylkit format')
+
+    parser.add_argument('-i', type=str, required=True,
+                        help='input file')
+    parser.add_argument('-o', type=str, required=True,
+                        help='output methylkit formated file')
+    parser.add_argument('--has_header', help="if input contains header", action='store_true')
+    parser.add_argument('--verbose', help="if output verbose info", action='store_true')
+    return parser.parse_args()
+
+
+if __name__ == '__main__':
+    args = parse_arguments()
+    if args.verbose:
+        set_log_debug_level()
+    else:
+        set_log_info_level()
+    logger.debug(f"args={args}")
+
+    df = pd.read_csv(args.i, sep='\t', index_col=None, header=True if args.has_header else None)
+    df.columns = ['chromosome', 'start', 'end', 'strand', 'NumOfAllCalls', 'NumOfModCalls', 'MethylFreq']
+    logger.debug(f"df={df}")
+    df['chrBase'] = df['chromosome'] + '.' + df['end'].astype(str)
+    df['chr'] = df['chromosome']
+    df['base'] = df['end']  # output base column is 1-based
+    df['strand'] = df['strand'].apply(lambda x: 'F' if x == '+' else 'R')
+
+    df['coverage'] = df['NumOfAllCalls']
+    df['freqC'] = df['MethylFreq'] * 100.0
+    df['freqT'] = (1 - df['MethylFreq']) * 100.0
+
+    df = df[['chrBase', 'chr', 'base', 'strand', 'coverage', 'freqC', 'freqT']]
+    logger.debug(f"new df={df}")
+
+    df.to_csv(args.o, sep='\t', index=False)
+    logger.info(f"save to {args.o}")