Creat data table of tracks on protein paint

usage: create_ppr_facet_table.py [-h] -f INPUT_TSV -d DIR --name NAME

create tracks

optional arguments:
  -h, --help            show this help message and exit
  -f INPUT_TSV, --input_tsv INPUT_TSV
                        tsv file (default: None)
  -d DIR, --dir DIR     genome browser HPC dir (default: None)
  --name NAME           your track name (default: None)

Example

../../_images/ppr_facet_table.PNG

Input

A tsv table summary of your data.

../../_images/ppr_facet_table_input.PNG

Output

The genome browser can be accessed through for example: https://ppr.stjude.org/?genome=hg19&block=1&tkjsonfile=yli11/PRPF19/track_collections/tracks.json

Usage

hpcf_interactive

module load conda3

source activate /home/yli11/.conda/envs/captureC

create_ppr_facet_table.py -f ppr.facet_table.tsv -d path_to_genomebrowser_HPC --name PRPF19_tracks

# if file_path in tsv not genome_browser path, then use --copy
create_ppr_facet_table.py -f chris2.tsv -d /home/yli11/dirs/genome_browser/yli11/Chris/ppr_table2 --name hub_table --copy

A simpler way to generate the Input tsv

This code glob all bw files in a given dir and output the tsv needed for ppr table.

It assumes each bw is named with pattern [sample_label].[level1_feature].antyhing_more.bw. Color will be randomly assigned. Level1 feature is currently fixed to either nuclease or control.

hpcf_interactive

glob_to_ppr_table.py my_dir out.tsv

code @ github.