sort_gff3

This function produces a sorted GFF3 file from an unsorted GFF3 file.
The output file will be sorted by Chromosome, Start, End (reverse) and feature (based on the precedency in feature tree)

internal

R utilities for gff files, either general feature format (GFF3) or gene transfer format (GTF) formatted files. This package includes functions for producing summary stats, check for consistency and sorting errors, conversion from GTF to GFF3 format, file sorting, visualization and plotting of feature hierarchy, and exporting user defined feature subsets to SAF format. This tool was developed by the BioinfoGP core facility at CNB-CSIC.

Juan Antonio Garcia-Martin

Rgff

R Utilities for GFF Files

Juan Carlos Oliveros

Rafael Torres-Perez

sort_gff3 function

<dl><dt>gffFile</dt>
<dd>Path to the input GFF3 file</dd>
<dt>outFile</dt>
<dd>Path to the output GFF3 file, if not provided the output will be the input path (without extension) with the suffix sorted.gff3</dd>
<dt>forceOverwrite</dt>
<dd>If output file exists, overwrite the existing file. (default FALSE)</dd></dl>

Arguments

Sorts a GFF3 file — sort_gff3

<dl>

<dt>gffFile</dt>
<dd>Path to the input GFF3 file</dd>


<dt>outFile</dt>
<dd>Path to the output GFF3 file, if not provided the output will be the input path (without extension) with the suffix sorted.gff3</dd>


<dt>forceOverwrite</dt>
<dd>If output file exists, overwrite the existing file. (default FALSE)</dd>

</dl>

sort_gff3: Sorts a GFF3 file

Description

Usage

Value

Arguments