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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,105 +1,90 @@ | ||
| #!/usr/bin/env python | ||
| # -*- coding: utf-8 -*- | ||
| """Count guides, optionally with reporter and alleles of a single sequencing sample.""" | ||
|
|
||
| import logging | ||
| import os | ||
| import sys | ||
|
|
||
| import bean | ||
| from bean.mapping.utils import ( | ||
| _check_arguments, | ||
| _get_input_parser, | ||
| _check_file, | ||
| _get_first_read_length, | ||
| _check_read_length, | ||
| ) | ||
|
|
||
| logging.basicConfig( | ||
| level=logging.INFO, | ||
| format="%(levelname)-5s @ %(asctime)s:\n\t %(message)s \n", | ||
| datefmt="%a, %d %b %Y %H:%M:%S", | ||
| stream=sys.stderr, | ||
| filemode="w", | ||
| ) | ||
| error = logging.critical | ||
| warn = logging.warning | ||
| debug = logging.debug | ||
| info = logging.info | ||
|
|
||
|
|
||
| _ROOT = os.path.abspath(os.path.dirname(__file__)) | ||
|
|
||
|
|
||
| def get_input_parser(): | ||
| """Get single-sample specific argument parser.""" | ||
| parser = _get_input_parser() | ||
| parser.add_argument( | ||
| "--R1", | ||
| type=str, | ||
| help="fastq file for read 1", | ||
| required=True, | ||
| default="Fastq filename", | ||
| ) | ||
| parser.add_argument( | ||
| "--R2", | ||
| type=str, | ||
| help="fastq file for read 2, sorted as the same name order as in --R1 file.", | ||
| required=True, | ||
| default="Fastq filename", | ||
| ) | ||
| return parser | ||
|
|
||
|
|
||
| def check_arguments(args, info_logger, warn_logger, error_logger): | ||
| args = _check_arguments( | ||
| args, info_logger=info, warn_logger=warn, error_logger=error | ||
| ) | ||
| _check_file(args.R1) | ||
| _check_file(args.R2) | ||
| read_length = _get_first_read_length(args.R1) | ||
| _check_read_length(args, read_length, warn) | ||
| return args | ||
|
|
||
|
|
||
| def main(): | ||
| parser = get_input_parser() | ||
| args = parser.parse_args() | ||
|
|
||
| args = check_arguments(args, info_logger=info, warn_logger=warn, error_logger=error) | ||
| args_dict = vars(args) | ||
|
|
||
| edited_from = args_dict["edited_base"] | ||
| match_target_pos = args_dict["match_target_pos"] | ||
|
|
||
| counter = bean.mp.GuideEditCounter(**args_dict) | ||
| counter.check_filter_fastq() | ||
|
|
||
| counter.get_counts() | ||
| if counter.count_reporter_edits: | ||
| counter.screen.uns["allele_counts"] = counter.screen.uns["allele_counts"].loc[ | ||
| counter.screen.uns["allele_counts"].allele.map(str) != "", : | ||
| ] | ||
| if match_target_pos: | ||
| base_editing_map = {"A": "G", "C": "T"} | ||
| edited_to = base_editing_map[edited_from] | ||
| counter.screen.get_edit_mat_from_uns( | ||
| edited_from, edited_to, match_target_pos | ||
| ) | ||
| counter.screen.write(f"{counter.output_dir}.h5ad") | ||
| counter.screen.to_Excel(f"{counter.output_dir}.xlsx") | ||
| info(f"Output written at:\n {counter.output_dir}.h5ad,\n {counter.output_dir}.xlsx") | ||
| info("All Done!") | ||
| print( | ||
| r""" | ||
| _ _ | ||
| / \ '\ _ | ||
| | \ \ __ ___ _ _ _ _| |_ | ||
| \ \ | / _/ _ \ || | ' \ _| | ||
| `.__|/ \__\___/\_,_|_||_\__| | ||
| """ | ||
| ) | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| main() | ||
| #!/usr/bin/env python | ||
| # -*- coding: utf-8 -*- | ||
| """Count guides, optionally with reporter and alleles of a single sequencing sample.""" | ||
|
|
||
| import logging | ||
| import os | ||
| import sys | ||
|
|
||
| import bean | ||
| from bean.mapping.utils import ( | ||
| _check_arguments, | ||
| _check_file, | ||
| _get_first_read_length, | ||
| _check_read_length, | ||
| ) | ||
|
|
||
| logging.basicConfig( | ||
| level=logging.INFO, | ||
| format="%(levelname)-5s @ %(asctime)s:\n\t %(message)s \n", | ||
| datefmt="%a, %d %b %Y %H:%M:%S", | ||
| stream=sys.stderr, | ||
| filemode="w", | ||
| ) | ||
| error = logging.critical | ||
| warn = logging.warning | ||
| debug = logging.debug | ||
| info = logging.info | ||
|
|
||
|
|
||
| _ROOT = os.path.abspath(os.path.dirname(__file__)) | ||
|
|
||
|
|
||
|
|
||
|
|
||
|
|
||
| def check_arguments(args, info_logger, warn_logger, error_logger): | ||
| args = _check_arguments( | ||
| args, info_logger=info, warn_logger=warn, error_logger=error | ||
| ) | ||
| _check_file(args.R1) | ||
| _check_file(args.R2) | ||
| read_length = _get_first_read_length(args.R1) | ||
| _check_read_length(args, read_length, warn) | ||
| return args | ||
|
|
||
|
|
||
| def main(args): | ||
| """Get the input data""" | ||
| print( | ||
| r""" | ||
| _ _ | ||
| / \ '\ _ | ||
| | \ \ __ ___ _ _ _ _| |_ | ||
| \ \ | / _/ _ \ || | ' \ _| | ||
| `.__|/ \__\___/\_,_|_||_\__| | ||
| """ | ||
| ) | ||
| args = check_arguments(args, info_logger=info, warn_logger=warn, error_logger=error) | ||
| args_dict = vars(args) | ||
|
|
||
| edited_from = args_dict["edited_base"] | ||
| match_target_pos = args_dict["match_target_pos"] | ||
|
|
||
| counter = bean.mp.GuideEditCounter(**args_dict) | ||
| counter.check_filter_fastq() | ||
|
|
||
| counter.get_counts() | ||
| if counter.count_reporter_edits: | ||
| counter.screen.uns["allele_counts"] = counter.screen.uns["allele_counts"].loc[ | ||
| counter.screen.uns["allele_counts"].allele.map(str) != "", : | ||
| ] | ||
| if match_target_pos: | ||
| base_editing_map = {"A": "G", "C": "T"} | ||
| edited_to = base_editing_map[edited_from] | ||
| counter.screen.get_edit_mat_from_uns( | ||
| edited_from, edited_to, match_target_pos | ||
| ) | ||
| counter.screen.write(f"{counter.output_dir}.h5ad") | ||
| counter.screen.to_Excel(f"{counter.output_dir}.xlsx") | ||
| info(f"Output written at:\n {counter.output_dir}.h5ad,\n {counter.output_dir}.xlsx") | ||
| info("All Done!") | ||
| print( | ||
| r""" | ||
| _ _ | ||
| / \ '\ _ | ||
| | \ \ __ ___ _ _ _ _| |_ | ||
| \ \ | / _/ _ \ || | ' \ _| | ||
| `.__|/ \__\___/\_,_|_||_\__| | ||
| """ | ||
| ) |
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