trace_assign_mask

Reliability status: stable

Output Files

For each trace file analyzed, the script generates:

1. [tracefile]_[label].ecsv: Trace table with the selected mask label assigned to traces that fall within the provided NUMPY mask file.

2. [tracefile]_[label]_mask_plot.[format]: Diagnostic plot showing the mask assignment result.

Examples

$ trace_assign_mask --input trace_file.ecsv --mask_file my_mask.npy --label mymask

This will apply the label mymask to traces falling within the masks of the file my_mask.npy. The output will be a trace file with the extension labeled.

Multiple mask files can be provided using piping.

$ ls my_traces*.ecsv | trace_assign_mask --mask_file my_mask.npy --pipe  --label mymask

In this case the mymask will be applied to multiple trace files.

Notes

Use trace_assign_mask to assign specific labels to chromatin traces in a trace table.

trace_assign_mask will load a trace file and a number of NUMPY-formatted mask files and assign labels. If a trace falls within a mask, then the mask label will be assigned to the corresponding column of the trace table. If a trace falls at the same time within multiple masks, multiple labels will be appended to the corresponding column of the trace table. If a trace falls within no mask, then the label column of the trace table will be kept empty.