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Improvements to parse.py #496

Merged
merged 10 commits into from
May 23, 2020
Merged

Improvements to parse.py #496

merged 10 commits into from
May 23, 2020

Commits on Mar 29, 2020

  1. Use str.translate to replace multiple characters 

    This is far more efficient than repeated calls to str.replace.
    @groutr
    groutr committed Mar 29, 2020
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  2. Fix up prettify.

    @groutr
    groutr committed Mar 29, 2020
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  3. Avoid loading all sequences into memory at once.

    @groutr
    groutr committed Mar 29, 2020
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  4. Use dictionaries for more cleaner field access.

    @groutr
    groutr committed Mar 29, 2020
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  5. More efficiently remove strain from tmp_meta

    @groutr
    groutr committed Mar 29, 2020
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  6. Check that strain exists before trying to remove it.

    @groutr
    groutr committed Mar 29, 2020
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Commits on May 15, 2020

  1. Manage file open/close outside of SeqIO. 

    Opening/Closing the output file here allows us to avoid loading all of
the input file into memory.
    @groutr
    groutr committed May 15, 2020
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  2. Nicer condition checks.

    @groutr
    groutr committed May 15, 2020
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  3. Iterate over intersection of tmp_meta and prettify_fields 

    No longer need to check if a field is in tmp_meta.
    @groutr
    groutr committed May 15, 2020
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  4. Fix dates on tmp_meta.

    @groutr
    groutr committed May 15, 2020
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