convert gRNA bed file to cutsite bed file

usage: to_cutsite_bed.py [-h] [-o OUTPUT] -f INPUT
                         (--offset OFFSET | --ABE | --CBE)

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        output file name, 4 columns (default: cutsite.bed)
  -f INPUT, --input INPUT
                        input bed file, 6 columns, chr, start, end, seq,
                        value, strand (default: None)
  --offset OFFSET       use cas9 cut site (e.g., -3) as gRNA score (default:
                        None)
  --ABE                 ABE mode not implemented (default: False)
  --CBE                 CBE mode not implemented (default: False)

Summary

This program will generate the bed file for cas9 cut positions. User is required to input the offset for Cas9 protein from PAM. spCas9 is -3.

Usage

Step 0: Load python version 2.7.13.

module load python/2.7.13

Step 1: Run the command

to_cutsite_bed.py -f gRNA.loci307.bed --offset -3 -o gRNA.cutsite.bed

Input and Output

==> gRNA.cutsite.bed <==
chr19   13215439        13215440        CTATGCGCAAGCCCGTGGCC
chr6    135501716       135501717       GACATGTGACAATACGACGG
chr6    135495900       135495901       GCCTGTAATCACAACACTTT
chr6    135376057       135376058       CGCATGCGCACTGCTGTGCA
chr19   12983944        12983945        AGTGGCCAAAGGGGGTGGGT
chr2    58274508        58274509        CGGCTTCTGGGTACCTTCCC
chr6    135376617       135376618       TCTCACTCACTTTGTCGCCC
chr19   13207655        13207656        GGCCCGGGCCGGAGCGTGCC
chr11   4167489 4167490 TTTACTACCTTCGAAAGTTG
chr11   5265111 5265112 AACTGCACACTGGATGGTGG

==> gRNA.loci307.bed <==
chr19   13215423        13215443        CTATGCGCAAGCCCGTGGCC    0       +
chr6    135501700       135501720       GACATGTGACAATACGACGG    0       +
chr6    135495884       135495904       GCCTGTAATCACAACACTTT    0       +
chr6    135376041       135376061       CGCATGCGCACTGCTGTGCA    0       +
chr19   12983928        12983948        AGTGGCCAAAGGGGGTGGGT    0       +
chr2    58274505        58274525        CGGCTTCTGGGTACCTTCCC    0       -
chr6    135376614       135376634       TCTCACTCACTTTGTCGCCC    0       -
chr19   13207639        13207659        GGCCCGGGCCGGAGCGTGCC    0       +
chr11   4167486 4167506 TTTACTACCTTCGAAAGTTG    0       -
chr11   5265108 5265128 AACTGCACACTGGATGGTGG    0       -

Comments

code @ github.