Comments (4)
ar0ch
commented on July 23, 2024
Requires importing six now, six docs.
Will compile into standalone stringMLST.py
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ar0ch
commented on July 23, 2024
In order to keep things simple, two binaries will be provided; this enhancement will likely be postponed.
The default stringMLST.py which is compatible with py2.6-3.4 and stringMLST-py35.py with compatibility only for py3.5+ syntax
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ar0ch
commented on July 23, 2024
Slight regression in time under <py2.7 because of iterator objects. In practice, looks like about a ~1sec penalty is incurred per sample. Will finish up tests and merge into master
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ar0ch
commented on July 23, 2024
c0f4533 brings the remaining code changes needed and the CI/tests are available locally for the time being
python --version; time ~/stringMLST/stringMLST.py --predict -1 ./tests/fastqs/ERR026529_1.fastq -2 ./tests/fastqs/ERR026529_2.fastq -p -P ./tests/testdb -t -o /dev/null; source deactivate; python --version; time ~/stringMLST/stringMLST.py --predict -1 ./tests/fastqs/ERR026529_1.fastq -2 ./tests/fastqs/ERR026529_2.fastq -p -P ./tests/testdb -t -o /dev/null
Python 2.7.12 :: Continuum Analytics, Inc.
~/stringMLST/stringMLST.py --predict -1 ./tests/fastqs/ERR026529_1.fastq -2 16.16s user 1.65s system 86% cpu 20.503 total
Python 3.5.2 :: Anaconda 4.2.0 (x86_64)
~/stringMLST/stringMLST.py --predict -1 ./tests/fastqs/ERR026529_1.fastq -2 17.03s user 1.94s system 90% cpu 20.982 total
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Related Issues (20)
- -z parameter says 500 is not an interger HOT 2
- Proxy issue? HOT 7
- Is this python 2 or python 3 ? HOT 2
- python error with --coverage HOT 13
- some samples came back with traceback error or empty result HOT 3
- How do you define an unknown allele in the profile file? HOT 5
- Formatting of the locus files ("Allele name in locus file should be seperated by '_' or '-'") HOT 3
- running time HOT 1
- Improved PubMLST download HOT 5
- '{speciesName}' does not exist on PubMLST HOT 1
- Kmer database building can't handle 'U' nucleotide HOT 1
- Missing stars in output
- Memory usage balloons when building rMLST kmer-database HOT 2
- Different allels predicted despite mapping showing they are the same HOT 5
- Catching errors with batch file handling
- Cut a 1.0.0 release
- IndexError: child index out of range HOT 4
- --getMLST command error: IndexError: child index out of range HOT 1
- ERROR while loading ST HOT 5
- --getMLST fails due to SSL self-signed cert error HOT 1
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