ChatterjeeLab / DPACMAN

Directory Structure

.
├── README.md
├── dpacman
│   ├── data
│   │   ├── README.md
│   │   ├── chip_atlas
│   │   │   ├── full_data_loading.py
│   │   │   └── smaller_data_loading.py
│   │   ├── remap
│   │   │   ├── analyze.py
│   │   └── tfclust
│   │       ├── analyze.py
│   │       ├── api_download.py
│   │       ├── combine.py
│   │       ├── download.py
│   │       ├── figures
│   │       │   ├── seq_lengths_box.png
│   │       │   ├── seq_lengths_flanked_box.png
│   │       │   ├── seq_lengths_flanked_hist.png
│   │       │   ├── seq_lengths_flanked_xlog_box.png
│   │       │   ├── seq_lengths_flanked_xlog_hist.png
│   │       │   ├── seq_lengths_hist.png
│   │       │   ├── seq_lengths_xlog_box.png
│   │       │   └── seq_lengths_xlog_hist.png
│   │       ├── hg38_success_download.log
│   └── data_files
│       ├── processed
│       │   └── tfclust
│       │       ├── hg19
│       │       │   ├── encRegTfbsClustered_hg19_chr1.csv
│       │       │   └── logs
│       │       │       ├── completed.txt
│       │       │       ├── completed_worker_0.txt
│       │       │       ├── worker_0.log
│       │       └── hg38
│       │           ├── encRegTfbsClustered_hg38_chr1.csv
│       │           └── logs
│       │               ├── completed.txt
│       │               ├── completed_worker_0.txt
│       │               ├── worker_0.log
│       └── raw
│           ├── chip_atlas
│           │   └── experimentList.tab
│           ├── genomes
│           │   ├── hg19
│           │   │   ├── hg19_chr1.json
│           │   └── hg38
│           │       ├── hg38_chr1.json
│           ├── remap
│           │   ├── reMap2022.bb
│           │   ├── reMap2022.bed
│           │   ├── remap2022_all_macs2_hg38_v1_0.bed.gz
│           │   └── remap2022_crm_macs2_hg38_v1_0.bed
│           └── tfclust
│               ├── encRegTfbsClusteredWithCells.hg19.bed
│               ├── encRegTfbsClusteredWithCells.hg38.bed
│               └── encRegTfbsClustered_data
│                   ├── hg19
│                   │   ├── hg19_encRegTfbsClustered_chr1.json
│                   └── hg38
│                       ├── hg38_encRegTfbsClustered_chr1.json
├── environment.yaml
├── setup.py
└── tree_output.txt

20 directories, 3089 files

In data_files subfolders, only representative files for certain chromosomes are shown. In reality, any file that contains the substring "_chr" exists for every chromosome in that genome. Genome hg38 has 711 chromosomes. Genome hg19 has 298 chromosomes. To reconstruct a full directory structure, run the following from DPACMAN

tree -I '__pycache__|*.egg-info|*.git' > tree.txt