commit 3a6b2b0 removes messages about mxCluster, which swamps output when generating an intron retention table for a few samples. In that case, there are only a few intron coverage files used as input, but I was using the input matrices from the whole cohort (e.g. 495 samples).
If this message is generally useful, it might be worth revisiting it. Consider adding a total number of mxClusters not found and an excerpt of several specific identifiers.
The commit silences mxCluster reports by changing print("mxCluster", sample, cluster, mxCluster) to pass on line 169 of splicedice/ir_table.py
Example output before change:
mxCluster TCGA-05-4395-01A chr1:44213663-44213748:+ chr1:44213550-44213708:+
mxCluster TCGA-05-4395-01A chr1:44213663-44213748:+ chr1:44213550-44213662:+
commit 3a6b2b0 removes messages about mxCluster, which swamps output when generating an intron retention table for a few samples. In that case, there are only a few intron coverage files used as input, but I was using the input matrices from the whole cohort (e.g. 495 samples).
If this message is generally useful, it might be worth revisiting it. Consider adding a total number of mxClusters not found and an excerpt of several specific identifiers.
The commit silences mxCluster reports by changing
print("mxCluster", sample, cluster, mxCluster)topasson line 169 of splicedice/ir_table.pyExample output before change: