endrebak
commented
1 year ago 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 bincounts, = 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!
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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
bincounts, = 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:
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]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!