We work on the legume Chickpea which genome has been recently released but it does not have a BSgenome package so far. I though I'd try and make one.
Following the vignette I have placed some FASTA chromosomes in a folder. I have started with a small example, so I have used just the first two chromosomes. I have two FASTA files named “Ca_chr1.fa” and “Ca_chr2.fa” located in
Then I have created a seed file ("cicer") which it is also included into that folder. The seed file looks like this :
Package: BSgenome.Carietinum.NCBI.ca1 Title: Cicer arietinum (Chickpea) full genome (NCBI version ASM33114v1) Description: Cicer arietinum (Chickpea) full genome as provided by NCBI (ASM33114v1, Jan. 2013) and stored in Biostrings objects. Version: 1.0 organism: Cicer arietinum species: Chickpea provider: NCBI provider_version: ASM33114v1 release_date: Jan. 2013 release_name: BGI-Shenzhen ASM33114v1 source_url: https://www.ncbi.nlm.nih.gov/assembly/GCF_000331145.1/#/def organism_biocview: Cicer_arietinum BSgenomeObjname: Carietinum seqnames: paste("Ca_", paste("chr", c(1:2), sep=""), sep="") seqs_srcdir: /Users/Cicer/seqs/
forgeBSgenomeDataPkg("path/to/cicer") i get this error:
Error in makeS4FromList("BSgenomeDataPkgSeed", x) : some names in 'x' are not valid BSgenomeDataPkgSeed slots (species) In addition: Warning message: In readLines(infile, n = 25000L) : incomplete final line found on './seqs/cicer'
Any suggestion it is greatly appreciated. Thanks.
> sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.4 (El Capitan) locale:  C attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods  base other attached packages:  BSgenome_1.38.0 rtracklayer_1.30.4 Biostrings_2.38.4 XVector_0.10.0  GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 IRanges_2.4.8 S4Vectors_0.8.11  BiocGenerics_0.16.1 loaded via a namespace (and not attached):  XML_3.98-1.5 Rsamtools_1.22.0 GenomicAlignments_1.6.3  bitops_1.0-6 futile.options_1.0.0 zlibbioc_1.16.0  futile.logger_1.4.3 lambda.r_1.1.9 BiocParallel_1.4.3  tools_3.2.3 Biobase_2.30.0 RCurl_1.95-4.8  SummarizedExperiment_1.0.2