Comments (4)
+1. It would be great to have cruzdb support python3. I will work on this at some point. Meanwhile, any pull request would be appreciated.
The Genome.url holds the template for the url. so that can be changed without modifying the code. Then we'd have to adjust create_url to do more careful checking (instead of just mysql:// prefix).
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The only problem is handling all the combinations that SQLAlchemy supports, IMO.
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Can just take an extra argument, eg dialect="oursql".
with the Genome.url as: url = "mysql+%(dialect)://%(user)s%(password)s@%(host)s/%(db)s"
with dialect default to mysqldb.
and adjust the matching which is currently:
if db.startswith(("sqlite://", "mysql://", "postgresql://")):
to use a regexp for all 3 like "^(sqlite|mysql|postgresql)(+[^:]+)://" # untested
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I'll try to get a PR done, thanks for the suggestions.
What about the unused "engine" parameter?
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Related Issues (20)
- Misleading docstring for dataframe() HOT 2
- Helpers to handle canonical forms of genes HOT 6
- add ncbi link when annotating
- Figure out what needs to be done for Python 3 compatiblity HOT 8
- sqlalchemy needs to be added to requirements HOT 1
- Is it possible to continue to mirror a database to the same destination if the connection breaks? HOT 4
- Gene ABR Cruzdb shows 8 different entries in RefGene whereas RefGene in UCSC shows 5 HOT 1
- one exon missing HOT 2
- Installation Issue HOT 6
- list of tables HOT 1
- invalid syntax? HOT 6
- cruzdb issues when called within Python 3 HOT 1
- ImportError: cannot import name MapperExtension HOT 2
- unable to use package after install HOT 1
- Add as PyPI package HOT 1
- access to bioconductor's TxDb's
- protein sequence
- report which exon from annotate
- script to create knownGene with name
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