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We don't have a symbol for the end of the metadata block. #26

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MatthewRalston opened this issue Jan 17, 2021 · 0 comments · Fixed by #27
Closed

We don't have a symbol for the end of the metadata block. #26

MatthewRalston opened this issue Jan 17, 2021 · 0 comments · Fixed by #27
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bug Something isn't working documentation Improvements or additions to documentation enhancement New feature or request good first issue Good for newcomers

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@MatthewRalston
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While reading the header in kmerdb.fileutil.KDBReader.__init__() we need to rstrip() from each block the tag, which should be defined in kmerdb/config.py, and be also used by the writer when writing the entire header to the file.

This can be used by kmerdb view to delineate the end of the header when reading the file. The real reason to use this is if the kdb input is being read from stdin, we need to gzip decompress it and iterate using with gzip.open(sys.stdin) as stdin and stdin.readline to append to a header string, until the following is encountered. Throw everything behind this into yaml.safe_parse, followed by schema validation. Then either construct the writer to write the profile to the new file or stdout

    kdb : can someone get me some sentries
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bug Something isn't working documentation Improvements or additions to documentation enhancement New feature or request good first issue Good for newcomers
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