-
Notifications
You must be signed in to change notification settings - Fork 585
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.
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
how to proceed #1
Comments
Good! So, I'd really like to jump in and work on ann_matrix as well, if you think this is efficient. Of course, I don't want to mess up what you had in mind.
*sorry, I simply forgot to add readwrite.py on thursday night, which caused master to be non-working since then, of course. with readwrite.py added, master now works just fine. I guess the only change you made to utils.py was adding the AnnData.from_dict(...) in the function read()? so one could use readwrite.py from master within ann_matrix. or just create readwrite.py again by cutting out everything related to reading/writing from utils and pasting it into the new module readwrite.py. |
Generally: What shall I do in order to merge ann_matrix as quickly as possible with the master branch? Starting from tomorrow, fiona would like to work on one tool using the nestorowa16 case i mentioned before. So if you allow me, I'll try to get everything running and polished tonight. |
sure, go ahead, i’m occupied today preparing my mitarbeitergespräch :D |
damn, I'm not fit enough to make ann_matrix work tonight. so, in order to get figures, analysis and a barebone code for fiona ready (we have a skype conference with fabian and the group in cambridge tomorrow at 11am, and fabian is quite pushy), i'll use the working master branch. let's discuss merging with ann_matrix in person during the next days. |
Updated read_10x_h5: - Renamed the original `read_10x_h5` as `_read_legacy_10x_h5`; - Added `_read_v3_10x_h5` to read the new Cell Ranger output format; - The new `read_10x_h5` determines the version of HDF5 input by the presence of the matrix key, and wraps the above two functions. In addition, it takes a `gex_only` argument which filters out feature barcoding counts from the outcome object when it is True (default). Otherwise, the full matrix will be retained. - For CR-v3, `feature_types` and `genome` were added into the outcome object as new attributes. Updated read_10x_mtx: - Renamed the original `read_10x_mtx` as `_read_legacy_10x_mtx`; - Added `_read_v3_10x_mtx` to read the new Cell Ranger output format; - The new `read_10x_mtx` determines the version of matrix input by the presence of the `genes.tsv` file under the input directory, and wraps the above two functions. In addition, it takes a `gex_only` argument which filters out feature barcoding counts from the outcome object when it is `True` (default). Otherwise, the full matrix will be retained. - For CR-v3, `feature_types` was added into the outcome object as a new attribute. Added test data and code for the revised functions. Note for the genome argument: - There is a genome argument in Scanpy's `read_10x_h5` function but not in `read_10x_mtx` as the genome was already specified by the path of input directory. The outcome object of the two functions should be the same which always take one genome at a time. - In this PR, when there are multiple genomes (e.g. Barnyard), `read_10x_mtx` always read them all, whereas `read_10x_h5` always need to specify one of them (mm10 by default). However, when `gex_only == False`, the `genome` argument will be ignored and the whole matrix will be read.
Let Scanpy read from Cell Ranger 3.0 outputs (#1)
AnnData
1cec418#commitcomment-20744162AnnData
. maybe fields namedvar_*
in the HDF5 will be var metadata and so on?*apart from things still crashing, especially the group plotting should be fixed (should probably be transformed to one
scatter
call with a list of all groups)The text was updated successfully, but these errors were encountered: