Comments (2)
Appeared to be a problem with chunksize
not being an integer, as well as file names being strings in python2 while byte literals in python3.
from cmash.
Appears to be fixed now
from cmash.
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
- Modularize StreamingQueryDNADatabase.py HOT 3
- 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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