On Wed, Jul 2, 2014 at 10:16 AM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Hi Dario,
>
> That error says that some of the attributes have been formatted in a way
> that leaves them uninterpretable by the parser.  But what really puzzles me
> is why you want to parse this track as a GTF file at all?  The UCSC hg19
> track is already available as a package here:
>
> http://www.bioconductor.org/packages/release/data/
> annotation/html/TxDb.Hsapiens.UCSC.hg19.knownGene.html
>
> And if that is not actually the track you are trying for, then perhaps you
> should just use the makeTranscriptDbFromUCSC() function instead?  That
> would be the more typical tool for making UCSC tracks into TranscriptDb
> objects.
>
> In contrast, using GTF or GFF files for making TranscriptDb objects is
> always a little risky because many of these files will not have been
> created with the intention of holding a transcriptome as data (which is the
> specific thing that a TranscriptDb object is meant to hold).  This is
> because the GTF and GFF file formats were not initially intended for the
> specific purpose of holding a transcriptome but were instead intended to be
> something more general.
>
>
Actually GTF (Gene Transfer Format) files are designed specifically for
representing gene models, and we have no excuse for not parsing them
correctly. There have been some tweaks to attribute parsing (I thought
limited to GFF3) in devel, so there may be a difference between Herve's
devel result and Dario's release result.  I'll try to find some time to
look into this.


> Hope this helps,
>
>
>  Marc
>
>
>
>
> On 07/02/2014 12:00 AM, Dario Strbenac wrote:
>
>> Hello,
>>
>> I used :
>>
>>  system.time(hg19 <- makeTranscriptDbFromGFF("/
>>> home/dario/data/Annotation/hg19.gtf", format = "gtf"))
>>>
>> Error in .parse_attrCol(attrCol, file, colnames) :
>>    Some attributes do not conform to 'tag value' format
>> Timing stopped at: 15.605 0.296 16.07
>>
>> I downloaded the GTF file from UCSC Table Browser. The table's name was
>> refGene. To me, it seems that the attributes are fine :
>>
>>  hg19table <- read.table("/home/dario/data/Annotation/hg19.gtf", sep =
>>> '\t', stringsAsFactors=FALSE)
>>> table(sapply(strsplit(hg19table[, 9], ' '), length))
>>>
>>       4
>> 967118
>>
>> I have R version 3.1.0 (2014-04-10) and GenomicFeatures 1.16.2
>>
>> --------------------------------------
>> Dario Strbenac
>> PhD Student
>> University of Sydney
>> Camperdown NSW 2050
>> Australia
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>
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