Hi Herve,

Thank you so much for your quick reply. Your vignette is pretty clear. I
think the problem is on my side. I just lack of experience on dealing with
this issue and maybe the file format doesn't fit. I sort of gave up using
the seed file but just using low level commands. I still have errors. I
really have no idea what is going on. Your help will be much appreciated.

Best,
Steve

1. with seed file, I got
> forgeBSgenomeDataPkg("./cflo_seed.R")
Error in as.list(.readSeedFile(x, verbose = verbose)) :
  error in evaluating the argument 'x' in selecting a method for function
'as.list'

2. with command forgeSeqlengthsFile,
> forgeSeqlengthsFile("cflo_v3.3.fold", prefix="",
suffix=".fa",seqs_srcdir=".", seqs_destdir=".", verbose=TRUE)
Saving 'seqlengths' object to compressed data file './seqlengths.rda'...
DONE
Warning messages:
1: In FUN("cflo_v3.3.fold"[[1L]], ...) :
  In file './cflo_v3.3.fold.fa': 24026 sequences found, using first sequence
only
2: In FUN("cflo_v3.3.fold"[[1L]], ...) :
  In file './cflo_v3.3.fold.fa': sequence description
"scaffold9scaffold12scaffold16scaffold2scaffold4scaffold20scaffold10scaffold11scaffold24scaffold1scaffold3scaffold6scaffold15scaffold28scaffold30scaffold22scaffold18scaffold21scaffold7scaffold32scaffold36scaffold13scaffold23scaffold39scaffold19scaffold41scaffold29scaffold37scaffold33scaffold45scaffold38scaffold17scaffold5scaffold46scaffold48scaffold31scaffold25scaffold51scaffold49scaffold44scaffold47scaffold54scaffold43scaffold55scaffold60scaffold35scaffold42scaffold63scaffold53scaffold50scaffold40scaffold67scaffold61scaffold69scaffold34scaffold70scaffold27scaffold73scaffold8scaffold75scaffold71scaffold74scaffold14scaffold66scaffold65scaffold80scaffold62scaffold76scaffold79scaffold85scaffold78scaffold86scaffold88scaffold81scaffold87scaffold26scaffold92scaffold93scaffold94scaffold59scaffold52scaffold84scaffold77scaffold89scaffold100scaffold97scaffold99scaffold64scaffold103scaffold90scaffold106scaffold56scaffold98scaffold109scaffold68sc
[... truncated]

3. with forgeSeqfiles,
> forgeSeqFiles("cflo_v3.3.fold", mseqnames=NULL, prefix="",
suffix=".fa",seqs_srcdir=".", seqs_destdir="./BSgenome", verbose=TRUE)
Loading FASTA file './cflo_v3.3.fold.fa' in 'cflo_v3.3.fold' object... DONE
Saving 'cflo_v3.3.fold' object to compressed data file
'./BSgenome/cflo_v3.3.fold.rda'... DONE
Warning message:
In .forgeSeqFile(name, prefix, suffix, seqs_srcdir, seqs_destdir,  :
  file contains 24026 sequences, using the first sequence only



2011/1/19 Hervé Pagès <hpages@fhcrc.org>

> Hi Steve,
>
> There are several things that look wrong with your seed file.
>
> 1. The # must be the first character in a line to make it a
>   line of comment (ignored).
>   For example, those 2 lines will certainly not be interpreted
>   as you might expect:
>
>
>     mseqnames: NA #paste("upstream", c("1000", "2000", "5000"), sep="")
>
>     source_url: NA #
> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
>
> 2. If you don't have multiple sequences, specify:
>
>     mseqnames: character(0)
>
> 3. As explained in the BSgenomeForge vignette, the default for
>   seqfiles_prefix is .fa so this won't work:
>
>     seqnames: "clof_v3.fa"
>
>   Unless your file is named clof_v3.fa.fa?
>   If your file is named clof_v3.fa, then you should specify:
>
>     seqnames: "clof_v3"
>
> 4. This doesn't look like a valid file of assembly gaps:
>
>
>     AGAPSfiles_name: clof_v3.fa.masked
>
>   Please refer to the BSgenomeForge vignette for what kind of masks
>   and what file formats are supported.
>
> 5. Having this
>
>
>     PkgExamples: Hsapiens
>            seqlengths(Hsapiens)
>            Hsapiens$chr1  # same as Hsapiens[["chr1"]]
>
>   in a seed file for clof obviously doesn't make sense and your
>   package won't pass 'R CMD check' because it will contain broken
>   examples.
>
> There might be other problems with your seed file. All you need to do
> is read and follow carefully the instructions described in the
> BSgenomeForge vignette. Let me know if things are not clear in the
> vignette and I'll try to improve it. Thanks!
>
> H.
>
>
>
> On 01/18/2011 05:32 PM, Steve Shen wrote:
>
>> Hi list,
>>
>> This wasn't sent out with a none registered ids. I have a problem with
>> forging a new BSgenome data package. The sequence data file is clof.v3.fa
>> and the mask file is clof.v3.fa.masked. Below are seed file, command,
>> error
>> and sessioninfo. Your help will be much appreciated.
>>
>> Thanks a lot,
>> Steve
>>
>> Package: BSgenome.Clof.yu.v3
>> Title: Clof (insects) full genome (version 3)
>> Description: Clof (insects) full genome as provided by YU (V3.3, Jan.
>> 2011)
>> # and will store in Biostrings objects.
>> Version: 1.0.0
>> organism: clof
>> species: insect
>> provider: YU
>> provider_version: Assembly V3.3
>> release_date: Jan, 2011
>> release_name: insects Genome Reference Consortium
>> source_url: NA # http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
>> organism_biocview: Clof
>> BSgenomeObjname: Clof
>> seqnames: "clof_v3.fa"
>> mseqnames: NA #paste("upstream", c("1000", "2000", "5000"), sep="")
>> nmask_per_seq: 2
>> #SrcDataFiles1: sequences: chromFa.zip, upstream1000.zip,
>> upstream2000.zip,
>> upstream5000.zip
>>     #from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
>> #SrcDataFiles2: AGAPS masks:
>> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz
>>     #RM masks:
>> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromOut.tar.gz
>>     #TRF masks:
>> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromTrf.tar.gz
>> PkgExamples: Hsapiens
>>     seqlengths(Hsapiens)
>>     Hsapiens$chr1  # same as Hsapiens[["chr1"]]
>> seqs_srcdir: /home/steve/Data/Genomes
>> masks_srcdir: /home/steve/Data/Genomes
>> AGAPSfiles_name: clof_v3.fa.masked
>>
>> The command, error and sessionInfo are below
>>
>>  forgeBSgenomeDataPkg("Clof_seed.R", seqs_srcdir=".", masks_srcdir=".",
>>>
>> destdir=".", verbose=TRUE)
>> Loading required package: Biobase
>>
>> Welcome to Bioconductor
>>
>>   Vignettes contain introductory material. To view, type
>>   'openVignette()'. To cite Bioconductor, see
>>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>>
>>
>> Attaching package: 'Biobase'
>>
>> The following object(s) are masked from 'package:IRanges':
>>
>>     updateObject
>>
>> Error in forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, masks_srcdir =
>> masks_srcdir,  :
>>   values for symbols NMASKPERSEQ are not single strings
>> In addition: Warning message:
>> In storage.mode(x$nmask_per_seq)<- "integer" : NAs introduced by coercion
>>
>>> sessionInfo()
>>>
>> R version 2.12.1 (2010-12-16)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] Biobase_2.6.1       BSgenome_1.18.2     Biostrings_2.18.0
>> [4] GenomicRanges_1.2.1 IRanges_1.8.8
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.12.1
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

	[[alternative HTML version deleted]]

