Blood data inquiry

usage: blood_data_inquiry.py [-h] [-j JID] -f BED_FILE [-o OUTPUT]
                             [--bam_file_list BAM_FILE_LIST]
                             [--bw_list BW_LIST] (--on_bw | --on_bam)

optional arguments:
  -h, --help            show this help message and exit
  -j JID, --jid JID     enter a job ID, which is used to make a new directory.
                        Every output will be moved into this folder. (default:
                        blood_data_inquiry_yli11_2019-10-03)
  -f BED_FILE, --bed_file BED_FILE
                        input bed file for featureCount (default: None)
  -o OUTPUT, --output OUTPUT
                        output file name (default: featureCount)
  --bam_file_list BAM_FILE_LIST
                        HemTools blood collection (default:
                        /home/yli11/HemTools/config/blood_ATAC.data)
  --bw_list BW_LIST     HemTools blood collection (default:
                        /home/yli11/HemTools/config/blood_ATAC.bw.list)
  --on_bw               extract values based on bw files (default: False)
  --on_bam              extract values based on bam files (default: False)

Summary

This is a suite of tools for users to query specific regions or genes among public blood datasets.

Output read counts over given bed. featureCount.tsv. Each row is one region from the input bed file. Each column is the bw/bam file name.

Input

Input format varies by different usage.

Bed format

Additional columns are OK. The first 3 columns have to be chr, start, end.

chr11   4167364 4167385
chr11   4167366 4167387
chr11   4167367 4167388
chr11   4167370 4167391

Usage

Signal values (bw) over input bed

blood_data_inquiry.py -f input.bed --on_bw

You can also input your own list of bw files by --bw_list option.

Read counts (bam) over input bed

blood_data_inquiry.py -f input.bed --on_bam

You can also input your own list of bam files by --bam_file_list option.

This output format is from featureCounts, the first 5 columns are: id, chr, start, end, strand

code @ github.