iRODS ranger

Install

bash pip install git+https://github.com/cellgeni/iranger.git

Usage

Load objects

```python import iranger

You can use your password directly

ir = iranger.setup(password='YouriRODSPasswordGoesHere')

...or alternatively put your password in a file and use that instead

ir = iranger.setup(passwordfile='~/mypassword_file')

load 10x cellranger output

adata = ir.read("/seq/26280/cellranger/cellranger302count26280FCAImmP7555847GRCh38-120")

load 10x spaceranger output

adata = ir.read("/seq/illumina/spaceranger/spaceranger130countWSSKNKCLsp12887269GRCh38-2020-A")

load 10x spaceranger output with raw counts

adataraw = ir.read("/seq/illumina/spaceranger/spaceranger130count_WSSKNKCLsp12887269GRCh38-2020-A", countfile="rawfeaturebcmatrix.h5")

load 10x cellranger-arc output

adata = ir.read("/seq/illumina/cellranger-arc/cellranger-arc101count1408ea687d742c7b571c62c7f441d372")

if you only want gene experession

adatagex = adata[:, adata.var["featuretypes"]=="Gene Expression"] ```

Embeded iRODS metadata

AnnData files will have an _irods key inside unstructured observations with the irods path and all the medata for the collection.

```python

adata.uns['irods'] { 'path': '/seq/26280/cellranger/cellranger302count26280FCAImmP7555847GRCh38-120', 'metadata': [{'name': 'librarytype', 'value': 'Chromium single cell'}, {'name': 'study', 'value': 'FCAImmunoP'}, {'name': 'studyaccessionnumber', 'value': 'EGAS00001002715'}, {'name': 'studyid', 'value': '5061'}, {'name': 'studytitle', 'value': 'FCAImmunoP'}, {'name': 'idrun', 'value': '26280'}, {'name': 'sample', 'value': 'FCAImmP7555847'}, {'name': 'sampleid', 'value': '3775200'}, {'name': 'analysistype', 'value': 'cellranger count'}, {'name': '10x:reference', 'value': '/nfs/srpipereferences/downloadedfrom10X/refdata-cellranger-GRCh38-1.2.0'}, {'name': '10x:pipeline', 'value': '/software/sciops/external/cellranger/3.0.2/cellranger'}, {'name': 'samplelims', 'value': 'SQSCP'}, {'name': 'sampleuuid', 'value': '8b7789d6-7abf-11e8-8cef-68b599768938'}] } ```

iRODS environment file

The package requires an irods_environment.json file present in the machine. The standard location is: bash ~/.irods/irods_environment.json

Should you whish to have it in a different location you'll have to be explicit about it, for example:

python ir = iranger.setup( irods_environment='/path/to/my/irods_environment.json', password_file='/safe/path/to/my_password_file' )

Search objects

```python import iranger

ir = iranger.setup(passwordfile='~/mypassword_file')

results = ir.find(sample='WSSKNKCLsp12887269')

for result in results: print(result['path']) for meta in result['metadata']: print(meta)

...

'/seq/illumina/spaceranger/spaceranger130countWSSKNKCLsp12887269GRCh38-2020-A'

{'samplecommonname': 'human'} {'librarytype': 'Chromium Visium'} {'study': 'HCA Skin Adult WSSS SpatialKCL'} {'studyaccessionnumber': 'EGAS00001005404'} {'studyid': '6551'} {'studytitle': 'HCA Skin Adult WSSS SpatialKCL'} {'idrun': '44928'} {'sample': 'WSSKNKCLsp12887269'} {'sampleaccessionnumber': 'EGAN00003542204'} {'sampleid': '8276456'} {'idrun': '44929'} {'10x:reference': '/nfs/srpipereferences/downloadedfrom10X/refdata-gex-GRCh38-2020-A'} {'analysistype': 'spaceranger count'} {'10x:pipeline': '/software/sciops/external/spaceranger/1.3.0/spaceranger'} {'samplelims': 'SQSCP'} {'sampleuuid': '7c579590-d060-11ec-a674-fa163eac3af7'} ```