Re: [base] array design GTF import - not 9 columns

[Nicklas N. <nic...@me...>]

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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