Sequence Searches

The sequence_searches tool is used determine if a sequence is present in a certain location around regions.

Note

This tool requires bedtools to be installed.

Usage and option summary

Usage:

PolTools PolTools sequence_searches [-h] regions_filename search [search ...]

Required Arguments	Description
Regions filename	Bed formatted file containing all the regions you want to quantify (must be centered on +1 nt). This file can be generated from the make_regions_file_centered_on_max_tss program
Search	Search region and sequence formatted as follows: (Sequence),(-/+)left:(-/+)right. Ex: TATA,-30:-20

Optional Arguments	Description
Search	Additional searches can be provided.

Behavior

sequence_searches will output the regions file provided with new columns for the searches containing True or False values.

For example:

$ head POLR2A_inr.bed
chr17   7484355 7484375 POLR2A  0       +

$ PolTools sequence_searches POLR2A_inr.bed GCTGC,-3:3
Chromosome      Left    Right   Gene    Score   Strand  GCTGC
chr17   7484355 7484375 POLR2A  0       +       True