auto_process_ngs.tenx.multiome
Utilities for working with 10x Genomics single cell multiome pipelines:
MultiomeLibraries
- class auto_process_ngs.tenx.multiome.MultiomeLibraries(filen)
Class to handle ‘10x_multiome_libraries.info’ files
These files link sample names in an analysis project with those in another project. They consist of tab-delimited lines of the form:
<LOCAL_SAMPLE> <REMOTE_SAMPLE>
where LOCAL_SAMPLE should be the name of a sample in the local project directory, and REMOTE_SAMPLE is a compound ID for a sample in a different project, of the form:
[RUN:]PROJECT/SAMPLE_NAME
In turn, RUN can be a run reference ID, a run name, or path to an analysis directory.
- linked_projects()
List the projects linked to this one
- linked_samples(sample)
List the remote samples associated with a local sample
- property local_samples
List the local sample names
- write_libraries_csv(sample, fastq_dir, library_type, filen=None)
Create a cellranger-arc libraries.csv file
The format is a header line of the form:
fastqs,sample,library_type
- Parameters:
sample (str) – local sample name
fastq_dir (str) – path to directory with the Fastqs for the sample
library_type (str) – name of the library type for the sample
filen (str) – optional, path to the output CSV file (defaults to ‘libraries.SAMPLE.csv’)