locsFromgff: Get genomic gene locations from the gff file
In YulongNiu/ProGenome: A package for processing prokaryotic genomes

Description Usage Arguments Details Value Author(s) See Also Examples

Get genomic genes location

GetLocsfgff(gffRawMat, genePrefix = character(0))

GetLocsfKEGGSpe(KEGGSpe)

GetLocsTag(annoStr)

ExtractLocs(gffRawMat)

download.SpeAnno(KEGGSpe, pattern, saveFolder)

`gffRawMat`	raw gff matrix.
`genePrefix`	prefix to locus gene names.
`KEGGSpe`	A KEGG species ID
`annoStr`	character strings of gff annotation, which is sperated by ';'.
`pattern`	A `character string` whether "gff" or "feature_table"
`saveFolder`	A folder to save gff and md5sum check files. If the folder does not exist, then creat a one at first.

GetLocsfgff(): get genomic gene location information from gff matrix. The whole genomic gene are divided by chromosomes and plasmids (if the organism has).

GetLocsfKEGGSpe(): get genes locus of KEGG species from NCBI gff files. It trys the RefSeq database at first; if RefSeq is not found, then changes to the database to GenBank. The prefix of locus name is the abbreviation of KEGG genomes.

ExtractLocs(): extract gene location from gff raw file.

download.SpeAnno(): download gff/feature_table and md5sum check files. If the md5sum check fails, download the files again until it passes.

GetLocsfgff(): a list of genomes containing gene location information. The locus_tags is used for the gene names.

GetLocsfKEGGSpe(): a list of genomes containing gene location information. The locus_tags is used for the gene names.

a matrix. Locus_tags, old_locus_tags will also be return if provided.

ExtractLocs(): 4 or 5-column matrix, 1st (or 1st and 2ed) is the locus_tags, the last three are start position, end postion, and DNA strand.

download.SpeAnno(): download the gff, feature_table, or md5sum files.

Yulong Niu niuylscu@gmail.com

read.gff read in gff files

## read in the dra (Deinococcus radiodurans R1) gff gz file in local disk
gzPath <- system.file("extdata", "dra.gff.gz", package = "ProGenome")
dragff <- read.gff(gzPath, isurl = FALSE, isgz = TRUE)

## only extract whole locus without genome division
locsRawMat <- ExtractLocs(dragff)

## whole locus divided by genomes and plasmids
locusList <- GetLocsfgff(dragff, genePrefix = 'dra:')

## get dra genomic locus through FTP URL
draLocs <- GetLocsfKEGGSpe('dra')

## two locus names for aac (Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446)
gzPath <- system.file("extdata", "aac.gff.gz", package = "ProGenome")
aacgff <- read.gff(gzPath, isurl = FALSE, isgz = TRUE)
locusList <- GetLocsfgff(aacgff, genePrefix = 'aac:')

## Not run: 
hxaLocs <- GetLocsfKEGGSpe('hxa')
csuLocs <- GetLocsfKEGGSpe('csu')
## End(Not run)
## Not run: 
download.SpeAnno('eco', 'gff', 'tmpEco')

## End(Not run)