tab2gff: creates a gff3-like table

Description Usage Arguments

View source: R/parsers.R

Description

Creates a table with columns as present in gff3 genome annotation files, including ;-separated attribute lists. Columns with RGB colors can be used to create snapgene-specific note in attributes.

Usage

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tab2gff(tab, columns = c(seqid = "chr", source = "source", type = "type",
  start = "start", end = "end", score = "score", strand = "strand", phase =
  "phase"), attributes = c(ID = "ID", Name = "name", Alias = "alias", Parent =
  "parent", color = "color"), notes, sep = "; ", source = c("chromosome",
  "plasmid"))

Arguments

tab

input table of genomic features with chromosome coordinate information

columns

a named string vector mapping from columns in tab (values) to the first 7 columns required for the gff3 file (names)

attributes

a named string vector mapping from columns in tab (values) to values in the attribute list; the names of the vector will become the key in the attribute list ("<key> = <value>") and attributes will be separated by arugment sep

notes

as arguments but output will be "note=<key>=<value>

sep

separator for attribute list

source

identifier of main source feature (chromosome)


raim/segmenTools documentation built on Nov. 9, 2018, 5:38 p.m.