trace_impute_genomic_coordinates

Reliability status: development

Assign genomic coordinates to a chromatin trace table. It assigns genomic coordinates (Chrom, Chrom_Start, Chrom_End) from the BED file to each row in the trace table based on the ‘Barcode #’ column.

usage: trace_impute_genomic_coordinates [-h] [--input INPUT] --bed BED
                                        [--output OUTPUT] [--pipe]
                                        [--auto-continue]

Named Arguments

--input

Path to the input trace file (ECSV format).

--bed

Path to the BED file containing genomic coordinates.

--output

Path to save the updated trace file.

--pipe

inputs Trace file list from stdin (pipe)

Default: False

--auto-continue

Automatically continue processing even with unmatched barcodes

Default: False

Usage example

trace_impute_genomic_coordinates --input trace_file.ecsv --bed bed_file.bed --output output_file.ecsv

BED file format

Warning

No header!

chrX            14785864        14789298                1
chrX            14789398        14792430                2
chrX            14792433        14795380                3
chrX            14795381        14798629                7
chrX            14799003        14802202                8
chrX            14802255        14805371                9
chrX            14805412        14809056                10
chrX            14809057        14812112                11
chrX            14812113        14814817                12
chrX            14814823        14818656                13
chrX            14824792        14829604                14

The last column should contain only numbers and should match the inputs in the Trace table which are themselves taken from the filenames processed by pyHiM