IRanges for neil.R

library(Rsamtools)
library(ShortRead)
gene_locations <- read.csv("gene_locations.csv")

gr <- GRanges(        seqnames      = gene_locations$Scaffold_name,
                      ranges        = IRanges(start=gene_locations$Gene.Start,end=gene_locations$Gene.Stop,names=gene_locations$locus_tag),
                      strand        = gene_locations$Gene.Strand)


#> head(gene_locations)
#  locus Gene.name  locus_tag Locus_evidence_level Scaffold.Number Scaffold_name
#1     2           SNOG_00002                    3               1    scaffold_1
#2     3           SNOG_00003                    2               1    scaffold_1
#3     4           SNOG_00004                    3               1    scaffold_1
#4     5           SNOG_00005                    3               1    scaffold_1
#5     6           SNOG_00006                    3               1    scaffold_1
#6     7           SNOG_00007                    3               1    scaffold_1
#  Gene.Start Gene.Stop Gene.Strand
#1      22020     24466           +
#2      25842     26135           +
#3      26209     29547           -
#4      30072     31598           +
#5      32042     33094           +
#6      33307     33642           -

#> gr
#GRanges with 100 ranges and 0 elementMetadata values
#             seqnames           ranges strand   |
#                <Rle>        <IRanges>  <Rle>   |
#SNOG_00002 scaffold_1   [22020, 24466]      +   |
#SNOG_00004 scaffold_1   [26209, 29547]      -   |
#SNOG_00005 scaffold_1   [30072, 31598]      +   |
#SNOG_00006 scaffold_1   [32042, 33094]      +   |
#SNOG_00007 scaffold_1   [33307, 33642]      -   |
#SNOG_00008 scaffold_1   [33962, 34992]      -   |
#SNOG_00010 scaffold_1   [39124, 40913]      -   |
#SNOG_00011 scaffold_1   [41484, 43978]      -   |
#SNOG_00012 scaffold_1   [45102, 45308]      +   |
#       ...        ...              ...    ... ...
#SNOG_00120 scaffold_1 [308457, 309143]      +   |
#SNOG_00121 scaffold_1 [310554, 310751]      -   |
#SNOG_00122 scaffold_1 [310817, 312067]      -   |
#SNOG_00126 scaffold_1 [315859, 316811]      -   |
#SNOG_00127 scaffold_1 [318645, 319559]      -   |
#SNOG_00128 scaffold_1 [319911, 321243]      +   |
#SNOG_00129 scaffold_1 [321461, 323775]      +   |
#SNOG_00130 scaffold_1 [323824, 324134]      +   |
#SNOG_00131 scaffold_1 [324364, 325175]      +   |