Comments (3)
Pretty happy with how this looks now. Everything is now in CMash/CMash/Query.py
that has to do with the StreamingQueryDNADatabase.py
all the tests (see #14) pushed in d77fb2a pass, so this should be good to go with a merge into master
. Will want to discuss with @ShaopengLiu1 @IsaacT1123 and @x-zang the changes, as now StreamingQueryDNADatabase.py
looks a whole heck of a lot different.
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Should rename Query
class to Construct
@dkoslicki
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Will now add a few unit tests for these newly created modules. See #14 for progress on this.
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Related Issues (20)
- Make python 3 compliant
- Testing environment HOT 9
- Improved classification time with KMC HOT 16
- Make a Conda/bioconda release of CMash HOT 3
- Update PyPi release of CMash
- Restructure repo so it's clear which approach is using the streaming, and which is using Bloom filters
- Multiple k-mer sizes bug HOT 2
- Multiple k-mer sizes confirmation and testing HOT 2
- Test k-mer frequency distribution idea HOT 2
- StreamingQueryDNA... may be case sensitive to sequences HOT 1
- In post-processing, find correct denominator
- Minor refactor of Query.py HOT 1
- Create script to demonstrate how to re-train CMash
- In MakeStreamingDNADatabase.py, don't require output directory to exist
- Gzipping all training files results in a nice reduction: add feature that allows scripts/modules to handle this
- For very large databases, creation of TST is slow and memory intensive HOT 6
- Ground truth computation is too slow for realistic data set sizes HOT 1
- Add KMC as requirement
- Is CMash metric? HOT 4
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