Dear colleagues,
I am looking for a python library equivalent to the one found in the bioconductor annotation package for TxDb object "TxDb.Hsapiens.UCSC.hg19.knownGene". Also, I am interested to know how essential this particular package is to you and among your fellows in the field of Genomics or in similar disciplines?
The biocondctor package direct URL: https://bioconductor.org/packages/release/data/annotation/html/TxDb.Hsapiens.UCSC.hg19.knownGene.html
much appreciated,
Nawaf.
In case there is no smarter way: you can extract the data from the database in R and save it as a text file which you can then read in python.
Jochen Wilhelm Thank you for your answer. I believe you could do both steps in python without needing to use R. The source code of the aforementioned R package does provide the database file (.sqlite) and so you could basically use python to extract the relevant data directly from the database using the python library "sqlite3" which what I eventually ended up doing.
Nawaf Alomran Thank you for this information. This is a smarter way :)
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