I just need to fix rtracklayer so that it handles the quoting. I'll work on
it now.

Michael


On Tue, Apr 2, 2013 at 10:22 AM, Sam McInturf <smcinturf@gmail.com> wrote:

> Michael,
>    Are the gene names you are referring to the ones in the last column?
>  gene_id "ATMG00010"; transcript_id "ATMG00010.1"; exon_number "1";
> gene_name "ORF153A"; ...
>
> What is an appropriate deliminator?  Can I just use a perl substitution
> for the new deliminator?
>
> Thanks
>
>
> On Mon, Apr 1, 2013 at 5:02 PM, Michael Lawrence <
> lawrence.michael@gene.com> wrote:
>
>> Thanks for the report. The issue is that there are semi-colons embedded
>> in the gene names.  This is perfectly valid, but rtracklayer is not smart
>> enough to check for quote escapes. I'll look into fixing this.
>>
>> Michael
>>
>>
>> On Mon, Apr 1, 2013 at 1:23 PM, Sam McInturf [guest] <
>> guest@bioconductor.org> wrote:
>>
>>>
>>> My name is Sam, a grad student at the University of Missouri, and I am
>>> having trouble importing my .gtf file using the rtracklayer function
>>> import().  My gtf file seems to have the 9 columns specified by the gtf
>>> format when looking at it in a text editor, but on import I have 9 columns
>>> labeled as "X1.", "X2",...,"X9." nearly all of the entries are NA.  In X1.
>>> there are 817 "1\" entries (of 474351), in X2. there are 534 "2\" and so
>>> on.  The .gtf file was downloaded from
>>> http://tophat.cbcb.umd.edu/igenomes.html
>>> Arabidopsis NCBI TAIR10 release, using the genes.gtf file generated
>>> after opening the .tar.gz.
>>>
>>> I import my file by
>>> myGTF <- "path/to/file.gtf"
>>> newGTF <- import(myGTF, asRangedData = FALSE)
>>>
>>> The way I read the import.gff manual, the .gtf extension will tell the
>>> function how to parse the file with out specifying version parameter.
>>>
>>> I am trying to follow the summarizeOverlaps() method of generating read
>>> counts from the GenomicRanges packages for differential expression using
>>> DESeq.
>>>
>>> Does anyone know what has happened, or more generally what can I do to
>>> import my file?
>>>
>>>  -- output of sessionInfo():
>>>
>>> > sessionInfo()
>>> R version 2.15.0 (2012-03-30)
>>> 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=C                 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] DESeq_1.8.3         locfit_1.5-8        Biobase_2.16.0
>>> [4] rtracklayer_1.16.3  Rsamtools_1.8.6     Biostrings_2.24.1
>>> [7] GenomicRanges_1.8.6 IRanges_1.14.3      BiocGenerics_0.2.0
>>>
>>> loaded via a namespace (and not attached):
>>>  [1] annotate_1.34.0      AnnotationDbi_1.18.0 bitops_1.0-4.1
>>>  [4] BSgenome_1.24.0      DBI_0.2-5            genefilter_1.38.0
>>>  [7] geneplotter_1.34.0   grid_2.15.0          lattice_0.20-6
>>> [10] RColorBrewer_1.0-5   RCurl_1.91-1         RSQLite_0.11.1
>>> [13] splines_2.15.0       stats4_2.15.0        survival_2.36-14
>>> [16] tools_2.15.0         XML_3.9-4            xtable_1.7-0
>>> [19] zlibbioc_1.2.0
>>>
>>>
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>>
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>>>
>>
>>
>
>
> --
> Sam McInturf
>

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