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 :
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.
organism: Cicer arietinum
release_date: Jan. 2013
release_name: BGI-Shenzhen ASM33114v1
seqnames: paste("Ca_", paste("chr", c(1:2), sep=""), sep="")
After running `
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.
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)
attached base packages:
 stats4 parallel stats graphics grDevices utils datasets methods
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
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