p3-get-features-in-regions

Return Features in Specific Genome Regions

p3-get-features-in-regions.pl [options] genomeCol contigCol startCol endCol

This script reads a list of genome coordinates and returns the features that overlap those coordinates. The standard input must contain four columns describing the coordinates– genome ID, contig ID, start location, and end location. Features that overlap the region will be retrieved and the specified feature attributes added to the end of each input record. Because multiple features may exist in a region, each input record may occur multiple times in the output.

Parameters

The positional parameters are the indices (1-based) or names of the genome ID column, the contig ID column, the starting-location column, and the ending-location column in the input.

The standard input can be overridden using the options in Input Options.

Additional command-line options are those given in Data Options plus the following.

• fields

List the available field names.