epic2-bw KeyError: 'required_flag' , doesn't appear in arg parser

[a-lahat]

Hi, I'm trying to run the following epic2-bw command and am getting a KeyError: 'required_flag'.
`epic2-bw --treatment TREATMENT --control CONTROL --genome GENOME --bin-size 100 --guess-bampe --log2fc-bigwig LOG2FC-BIGWIG-FILE

Traceback (most recent call last):
File ".../bin/epic2-bw", line 192, in
main(args)
File ".../lib/python3.7/site-packages/epic2/bigwig.py", line 113, in main
treatment_ranges = files_to_coverage(args["treatment"], args)
File ".../lib/python3.7/site-packages/epic2/bigwig.py", line 75, in files_to_coverage
ranges = file_to_ranges(f, args, "ChIP")
File ".../lib/python3.7/site-packages/epic2/bigwig.py", line 44, in file_to_binned_ranges
bin_counts, _ = files_to_bin_counts([f], args, datatype)
File "epic2/src/reads_to_bins.pyx", line 218, in epic2.src.reads_to_bins.files_to_bin_counts
File "epic2/src/reads_to_bins.pyx", line 250, in epic2.src.reads_to_bins.files_to_bin_counts
KeyError: 'required_flag'`

I noticed that:

1. the --required-flag flag doesn't exist in the epic2-bw usage:
   usage: epic2-bw [-h] --treatment TREATMENT [TREATMENT ...] [--control CONTROL [CONTROL ...]] [--raw] [--bigwig BIGWIG] [--individual-log2fc-bigwigs INDIVIDUAL_LOG2FC_BIGWIGS] [--chip-bigwig CHIP_BIGWIG] [--input-bigwig INPUT_BIGWIG] [--log2fc-bigwig LOG2FC_BIGWIG] [--genome GENOME] [--keep-duplicates] [--bin-size BIN_SIZE] [--fragment-size FRAGMENT_SIZE] [--chromsizes CHROMSIZES] [--guess-bampe] [--mapq MAPQ] [--example] [--version]

2. In ".../bin/epic2-bw" there is no "--required-flag" arg in the arg parser.

I'd be very grateful to hear from you on how to run the above command so that it passes this indexing:
cpp_tags = read_bampe(f, drop_duplicates, args["mapq"], args["required_flag"], args["filter_flag"])

Many thanks!

[endrebak]

It seems to be missing from epic2-bw. It is here: https://github.com/biocore-ntnu/epic2/blob/master/bin/epic2#L139 Would you be able to submit a PR?

…

On Mon, Jan 9, 2023 at 2:41 PM a-lahat ***@***.***> wrote: Hi, I'm trying to run the following epic2-bw command and am getting a KeyError: 'required_flag'. `epic2-bw --treatment TREATMENT --control CONTROL --genome GENOME --bin-size 100 --guess-bampe --log2fc-bigwig LOG2FC-BIGWIG-FILE Traceback (most recent call last): File ".../bin/epic2-bw", line 192, in main(args) File ".../lib/python3.7/site-packages/epic2/bigwig.py", line 113, in main treatment_ranges = files_to_coverage(args["treatment"], args) File ".../lib/python3.7/site-packages/epic2/bigwig.py", line 75, in files_to_coverage ranges = file_to_ranges(f, args, "ChIP") File ".../lib/python3.7/site-packages/epic2/bigwig.py", line 44, in file_to_binned_ranges bin_counts, _ = files_to_bin_counts([f], args, datatype) File "epic2/src/reads_to_bins.pyx", line 218, in epic2.src.reads_to_bins.files_to_bin_counts File "epic2/src/reads_to_bins.pyx", line 250, in epic2.src.reads_to_bins.files_to_bin_counts KeyError: 'required_flag'` I noticed that: 1. the --required-flag flag doesn't exist in the epic2-bw usage: usage: epic2-bw [-h] --treatment TREATMENT [TREATMENT ...] [--control CONTROL [CONTROL ...]] [--raw] [--bigwig BIGWIG] [--individual-log2fc-bigwigs INDIVIDUAL_LOG2FC_BIGWIGS] [--chip-bigwig CHIP_BIGWIG] [--input-bigwig INPUT_BIGWIG] [--log2fc-bigwig LOG2FC_BIGWIG] [--genome GENOME] [--keep-duplicates] [--bin-size BIN_SIZE] [--fragment-size FRAGMENT_SIZE] [--chromsizes CHROMSIZES] [--guess-bampe] [--mapq MAPQ] [--example] [--version] 2. In ".../bin/epic2-bw" there is no "--required-flag" arg in the arg parser. I'd be very grateful to hear from you on how to run the above command so that it passes this indexing: cpp_tags = read_bampe(f, drop_duplicates, args["mapq"], args["required_flag"], args["filter_flag"]) Many thanks! — Reply to this email directly, view it on GitHub <#68>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEHURUQZQMC6H45XFHJMX5LWRQIPXANCNFSM6AAAAAATVOHZY4> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[a-lahat]

Happy to.
Im getting - remote: Permission to biocore-ntnu/epic2.git denied to a-lahat.
Could you help with the permission and I'll push the PR?
Thanks