Skip to content

TASK-2428 - Pycellbase cbtools not working for cellbase v5 #631

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
dapregi wants to merge 1 commit into
base: release-5.2.x
Choose a base branch
from
Draft

TASK-2428 - Pycellbase cbtools not working for cellbase v5 #631

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 6 additions & 1 deletion cellbase-client/src/main/python/README.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -202,7 +202,12 @@ ID converter
````````````

This tool annotates genomic features with all their associated IDs, making use of 74 different sources for human, including most common databases such as Ensembl, NCBI, RefSeq, Reactome, OMIM, PDB, miRBase or UniProt among others.
In addition, it supports heterogeneous input files with IDs from different sources.

.. code-block:: bash

$ cbtools.py xref BRCA1

A file with multiple variants can also be used.

.. code-block:: bash

Expand Down
5 changes: 2 additions & 3 deletions cellbase-client/src/main/python/pycellbase/cbconfig.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,8 @@

_DEFAULT_CONFIG = {
"species": "hsapiens",
"version": "v4",
"rest": {"hosts": ["http://bioinfo.hpc.cam.ac.uk:80/cellbase",
"https://bioinfo.hpc.cam.ac.uk:80/cellbase"]}
"version": "v5",
"rest": {"hosts": ["https://ws.zettagenomics.com/cellbase"]}
}


Expand Down
Loading