Aim

Sometimes different properties of features need to be examined, for example, the proportion of a genomic region covered by . Overlap features with genomic regions adding an additional column with information depending on the feature class (binary, numeric, integer...).

Input

Two BED files (genomic regions and features) with at least three cols:

• Chromosome ID
• Genomic region start
• Genomic region end

Some classes demand the input feature BED file to have one aditional column.

Usage

bash custom_intersect.sh genomic_regions.bed feature.bed class

Options

Specify the feature class. 6 classes are accepted:

• Binary
• Ratio
• Ratio.value
• Integer (count)
• Numeric
• Numeric.sum

Example

Input

> genomic_regions.bed
chrA01  1  100
chrA01  101  200
chrA01  201  300
chrA01  301  400
chrA02  1  101

> feature.bed
chrA01  1  5
chrA01  12  14
chrA01  189  192
chrA01  432  433

Execution as ratio

bash custom_intersect.sh genomic_regions.bed feature.bed ratio

Output as ratio

> genomic_regions.bed
chrA01  1  100  0.06
chrA01  101  200  0.03
chrA01  201  300  0.00
chrA01  301  400  0.00
chrA02  1  101  0.00

Execution as integer

bash custom_intersect.sh genomic_regions.bed feature.bed integer

Output as integer

> genomic_regions.bed
chrA01  1  100  6
chrA01  101  200  3
chrA01  201  300  0
chrA01  301  400  0
chrA02  1  101  0