Question: Error while forge Bsgenome
0
gravatar for Marcin Grzybowski
4.2 years ago by
Poland
Marcin Grzybowski0 wrote:

Hi,

i'm trying to forge Bs genome data package with maize genome

Following the vignette I downloaded FASTA file (each for one chromosome) and put it into one folder:

marcin@marcin:/media/marcin/ngs/maizeGenome/seed$ ls
chr10.fa  chr2.fa  chr4.fa  chr6.fa  chr8.fa  maize
chr1.fa   chr3.fa  chr5.fa  chr7.fa  chr9.fa

I also create seed file:

Package: BSgenome.Zmays.NCBI.AGPv3
Title: Full genome sequences for Zea mays (AGPv3)
Description: Full genome sequences for Zea mays
Version: 1.0.0
organism: Zea mays
common_name: maize
provider: NCBI
provider_version:
release_date: Oct. 2015
release_name: MaizeGDB
source_url: http://www.ncbi.nlm.nih.gov/genome/?term=zea+mays
organism_biocview: Zea_mays
BSgenomeObjname: Zmays
seqnames: paste("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10")
seqs_srcdir: /media/marcin/ngs/maizeGenome/seed

Unfortunately, after running:

forgeBSgenomeDataPkg("/media/marcin/ngs/maizeGenome/seed/maize")

I got error:

Creating package in ./BSgenome.Zmays.NCBI.AGPv3
Error in getSeqSrcpaths(seqname, prefix = prefix, suffix = suffix, seqs_srcdir = seqs_srcdir) :
  file(s) not found: /media/marcin/ngs/maizeGenome/chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10.fa

I will be grateful for help.

Marcin

 

bsgnome forge • 727 views
ADD COMMENTlink modified 4.2 years ago by Hervé Pagès ♦♦ 14k • written 4.2 years ago by Marcin Grzybowski0
Answer: Error while forge Bsgenome
1
gravatar for Hervé Pagès
4.2 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:

Use c() instead of paste():

## Not what you want:
paste("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10")
# [1] "chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10" # a single string!

## What you want (1 string per FASTA file):
c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10")
#  [1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8"  "chr9" 
# [10] "chr10"

Cheers,

H.

 

ADD COMMENTlink written 4.2 years ago by Hervé Pagès ♦♦ 14k

Thx a lot!

Marcin

ADD REPLYlink written 4.2 years ago by Marcin Grzybowski0
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