Thanks for the quick reply Nicklas,
We'll strip out the comments for now and keep on testing.
cheers,
Bob
On Mon, May 26, 2014 at 7:37 AM, Nicklas Nordborg <
nicklas.nordb...@med.lu.se> wrote:
> Thanks for testing this. It feels like it was a long time ago this was
> implemented and we have not really started to use it yet. Anyway, you
> are correct that the problem is something deeper than the usual importer.
>
> To make GTF files parsable by the regular importers, there is a
> pre-parsing step that add headers and rewrites the "attributes" column
> (column 9) so that each attribute value is tab-separated instead of
> semicolon-separated.
>
> It is the pre-parser that complains if a line doesn't have at least 9
> columns. I checked the code and found a "TODO" comment about
> implementing support for comments, but for some reason it has been
> overlooked. It should be easy enough to implement this, and I can
> probably fix this for the next (BASE 3.3) release.
>
> But for now, the importer will choke on anything that is not a "Field"
> line as described by http://www.ensembl.org/info/website/upload/gff.html
>
> /Nicklas
>
>
> On 2014-05-23 18:17, Bob MacCallum wrote:
> > Hi all,
> >
> > [mods please delete the mail I sent from my gmail account, or add me
> > with that account but with no delivery, thank]
> >
> > Just upgraded from 2->3 and now trying out the NGS feaures. Quick
> > question about GTF import for array designs...
> >
> > When doing array design->import the importer is complaining:
> >
> > "Error: A line must have at least 9 columns, at line: 1"
> > stack trace below
> > (using GTF reporter map importer (version 3.2.5-dev))
> >
> > The same error came up when we first created the array design (because I
> > checked the "validate files" box.
> >
> > I know the first line has fewer columns because it has some # commented
> > lines
> >
> > so in the importer configuration I configured the "Ignore" field like
> > this: ^#.*
> >
> > But still the same error...
> >
> > Even if I set Default error handling = skip it's the same. Seems to be
> > something deeper than the usual tab delimited importer parser settings.
> >
> > I guess we should make a new GTF file with no comments but I just wanted
> > to check if this was the intended behaviour?
> >
> > cheers,
> > Bob
> >
> >
> >
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