p3-feature-gap

Compute Gap Between Feature Pairs

p3-feature-gap [options] <featurePairFile

This script reads in a list of feature pairs and computes the gap between the features. If the features are on different contigs or belong to different genomes, the gap will be listed as 2 billion. This behavior can be overridden with a command-line option.

Parameters

There are no positional parameters.

The standard input can be specified using Input Options. The input column can be specified using Column Options. The following additional command-line options can be specified.

• inf

Value to return for an infinite gap (different contigs or genomes). The default is 2000000000.

• col2

Name or index of the column containing the ID of the second feature. The default is -1, which is the second-to-last column.

Example

p3-echo -t f1.patric_id -t f2.patric_id “fig|1302.21.peg.966” “fig|1302.21.peg.1019” | p3-feature-gap

f1.patric_id f2.patric_id gap fig|1302.21.peg.966 fig|1302.21.peg.1019 55253