added new subcommand to merge TFBS in a subset of regions #268
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hschult
requested changes
Jun 5, 2024
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| required.add_argument("--bindetect", "--TFBS", "--input", type=os.path.abspath, dest="tfbs", help="Path to the output directory of BINDetect containing all TFBS files.") | ||
| required.add_argument("--regions", help="Path to the query regions bed file.", type=os.path.abspath, dest="regions") |
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| required.add_argument("--bindetect", "--TFBS", "--input", type=os.path.abspath, dest="tfbs", help="Path to the output directory of BINDetect containing all TFBS files.") | |
| required.add_argument("--regions", help="Path to the query regions bed file.", type=os.path.abspath, dest="regions") | |
| required.add_argument("--bindetect", "--TFBS", "--input", required=True, type=os.path.abspath, dest="tfbs", help="Path to the output directory of BINDetect containing all TFBS files.") | |
| required.add_argument("--regions", required=True, help="Path to the query regions bed file.", type=os.path.abspath, dest="regions") |
You have to add required=True otherwise parameters are considered optional.
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| #Required arguments | ||
| required = parser.add_argument_group('Required arguments') | ||
| required.add_argument("--bindetect", "--TFBS", "--input", type=os.path.abspath, dest="tfbs", help="Path to the output directory of BINDetect containing all TFBS files.") |
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Why did you add three different names for this parameter? This could be confusing for some. Consider choosing one and an abbreviation e.g. input and i
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| #Optional arguments | ||
| optional = parser.add_argument_group('Optional arguments') | ||
| optional.add_argument( "--output", default='./merged_TFBS_subset.xlsx', help="Path for output file. If file name ends with .bed, no header column will be added.", type=os.path.abspath, dest="output") |
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- Use a plain txt file as default output for example tsv or bed.
- Also, add the default value to the help message. See the parameters of other functions, match their style and check if other parameters should have a default in the help description.
| optional.add_argument("--TFs", help="Path to the file containing the list of TFs to subset.", type=os.path.abspath, dest="TF", default=None) | ||
| optional = add_logger_args(optional) | ||
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| return(parser) |
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| return(parser) | |
| return(parser) | |
Git wants to have an empty line at the end of each file.
| parser.print_help() | ||
| sys.exit() | ||
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| run_submerge(args.tfbs, args.regions, args.TF, args.output, args.verbosity) |
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Why not?
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| run_submerge(args.tfbs, args.regions, args.TF, args.output, args.verbosity) | |
| run_submerge(args) |
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| command = f"bedtools intersect -a {regions} -b {headless_file} -wa -wb" | ||
| intersection = subprocess.check_output(command, shell=True).decode("utf-8") | ||
| all_intersections += intersection |
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| if args.output.endswith(".bed"): | ||
| pass | ||
| else: |
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| if args.output.endswith(".bed"): | |
| pass | |
| else: | |
| if not args.output.endswith(".bed"): |
| logger.end() | ||
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| def main(): |
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The main function is not really needed. Since it is not much you could just add the code to the "main-if". However, this comes down to preference consider this a comment and keep it as you like.
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| # remove 'chr' str from all chr columns TODO not optimal as contigs may be named differently, i.e. 'contig' or 'chrIV' | ||
| df["query chr"] = df["query chr"].str.replace("chr", "") | ||
| df["TFBS_chr"] = df["TFBS_chr"].str.replace("chr", "") |
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If you do this for sorting purposes alone consider using the key parameter instead.
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| df.to_csv(args.output, sep="\t", index=False) | ||
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| if args.output.endswith(".xlsx"): | ||
| df = pd.read_csv(args.output, sep="\t") | ||
| df.to_excel(args.output, index=False) |
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You are writing the output file then you read it back in and then you overwrite it as an excel file? What? Please explain :D
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