[BioC] (BSgenome) forgeBSgenomeDataPkg for Sus scrofa problem
Elisabetta Manduchi
manduchi at pcbi.upenn.edu
Fri Oct 7 20:21:14 CEST 2011
Hello,
I'm trying to build a data package for Sus scrofa with BSgenome (R
version 2.13.2 and BSgenome version 1.20.0).
At the bottom of this email I've copied my seed file.
I've downloaded the sequence files from UCSC and checked the md5sums. I've
also downloaded the gap.txt and masks files (chr*.fa.out and chr*.bed)
from UCSC (but no md5sums were provided).
I've followed the instructions from
http://bioconductor.org/packages/2.8/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf
and I'm getting the following error
---
> forgeBSgenomeDataPkg("./BSgenome.Sscrofa.UCSC.susScr2-seed")
Error in forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, masks_srcdir =
masks_srcdir, :
values for symbols NMASKPERSEQ are not single strings
---
Can you advice on what the problem might be?
Thanks,
Elisabetta
*SEED file BSgenome.Sscrofa.UCSC.susScr2-seed*
Package: BSgenome.Sscrofa.UCSC.susScr2
Title: Sus scrofa (Pig) full genome (UCSC version susScr2)
Description: Sus scrofa (Pig) full genome as provided by UCSC (susScr2,
Nov. 2009)
Version: 0.1-0
Author: Elisabetta Manduchi <manduchi at pcbi.upenn.edu>
Maintainer: Elisabetta Manduchi <manduchi at pcbi.upenn.edu>
License: GPL-3
organism: Sus scrofa
species: Pig
provider: UCSC
provider_version: susScr2
release_date: Nov. 2009
release_name: SGSC Sscrofa9.2
source_url: http://hgdownload.cse.ucsc.edu/goldenPath/susScr2/
organism_biocview: Sus_scrofa
BSgenomeObjname: Sscrofa
seqnames: paste("chr", c(1:18, "X", "M"), sep="")
circ_seqs: "chrM"
SrcDataFiles1: sequences: all the chr*.fa.gz files from ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/chromosomes/
SrcDataFiles2: AGAPS masks: the gap.txt.gz file from http://hgdownload.cse.ucsc.edu/golden
Path/susScr2/database/; RM masks: http://hgdownload.cse.ucsc.edu/goldenPath/susScr2/bigZip
s/chromOut.tar.gz;TRF masks: http://hgdownload.cse.ucsc.edu/goldenPath/susScr2/bigZips/chr
omTrf.tar.gz
seqs_srcdir: /mnt/files/cbil/data/cbil/UHTS/Davies/AAvsDT_DNAmethyl/working_dir/MEDIPS/BSgenome.Sscrofa.UCSC.susScr2/seqs
masks_srcdir: /mnt/files/cbil/data/cbil/UHTS/Davies/AAvsDT_DNAmethyl/working_dir/MEDIPS/BS
genome.Sscrofa.UCSC.susScr2/masks
AGAPSfiles_type: gap
AGAPSfiles_name: gap.txt
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