Looks like SCAN.UPC has implemented yet another GTF parser....


On Thu, Jun 5, 2014 at 11:27 AM, Beth Wilmot <wilmotb@ohsu.edu> wrote:

>  My code is:
>
>
> ParseMetaFromGtfFile("mm10/Mus_musculus.GRCm38.73.gtf",fastaFilePattern="mm10/Mus_musculus.GRCm38.73.fa",outFilePath="mm10/GRCh38_Annotation.txt",featureTypes=c("protein_coding"),attributeType="gene_id")
>
>
>
> Thanks,
> Beth
>
>
>
> *From:* Michael Lawrence [mailto:lawrence.michael@gene.com]
> *Sent:* Thursday, June 05, 2014 11:23 AM
> *To:* Beth Wilmot [guest]
> *Cc:* bioconductor@r-project.org; Beth Wilmot; SCAN.UPC Maintainer
> *Subject:* Re: [BioC] ParseMetaFromGtfFile is.na() error
>
>
>
> What was the actual code that produced the error? It looks like this is
> from GenomicFeatures?
>
>
>
> On Thu, Jun 5, 2014 at 10:38 AM, Beth Wilmot [guest] <
> guest@bioconductor.org> wrote:
>
> Hi,
> I am using SCAN.UPC and trying to create an annotation file from one
> concatenated GRCm38.73 fasta file.  I have the matched GRCm38.73.gtf file.
>  The .gtf file parsing halts near the end of the file and the following
> error message appears and no output file is generated.  Thanks, Beth
>
> ...
> Done parsing 1140000 lines from /Mus_musculus.GRCm38.
> 73.gtf
> Warning message:
> In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
>
>  -- output of sessionInfo():
>
>
>
> > sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-unknown-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=en_US.UTF-8    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] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>  [1] SCAN.UPC_2.6.0       sva_3.10.0           mgcv_1.7-29
>  [4] nlme_3.1-117         corpcor_1.6.6        foreach_1.4.2
>  [7] affyio_1.32.0        affy_1.42.2          GEOquery_2.30.0
> [10] oligo_1.28.2         Biostrings_2.32.0    XVector_0.4.0
> [13] IRanges_1.22.2       oligoClasses_1.26.0  Biobase_2.24.0
> [16] BiocGenerics_0.10.0  limma_3.20.1         Rsubread_1.14.0
> [19] BiocInstaller_1.14.2
>
> loaded via a namespace (and not attached):
>  [1] affxparser_1.36.0     bit_1.1-12            codetools_0.2-8
>  [4] DBI_0.2-7             ff_2.2-13             GenomeInfoDb_1.0.1
>  [7] GenomicRanges_1.16.0  grid_3.1.0            iterators_1.0.7
> [10] lattice_0.20-29       MASS_7.3-31           Matrix_1.1-3
> [13] preprocessCore_1.26.1 RCurl_1.95-4.1        splines_3.1.0
> [16] stats4_3.1.0          tools_3.1.0           XML_3.98-1.1
> [19] zlibbioc_1.10.0
> >
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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