[Bioc-devel] Patch to GFF3 reader in rtracklayer

Ok, I put the patch in a Github gist, since the list seems to not like patch
as an attachment:

https://gist.github.com/3490557

On 08/27/2012 09:32 AM, Ryan C. Thompson wrote:

It looks like the attachment was scrubbed from my initial message. Here is
another attempt to send it.

On Mon 27 Aug 2012 08:50:03 AM PDT, Ryan C. Thompson wrote:

Hi all,

I recently found that rtracklayer's GFF3 file read was unable to read
GFF3 files produced by Cufflinks. I tracked the problem down to the
occurrence of equals signs in tag values. For example, the following
line was problematic:

C123300344      Cufflinks       transcript      1       132 . -
.

ID=TCONS_00000337;geneID=XLOC_000337;oId=ENSMMUP00000032229;nearest_ref=ENSMMUP00000032229;class_code==;tss_id=TSS337;p_id=P1


due to the "class_code==" part (the value of the class code is
actually an equals sign). Obviously the bug occurs because "strsplit"
doesn't stop after the first split, but keeps splitting at subsequent
occurrences of the separator. I have modified the reader to be able to
handle this case, which as far as I know is perfectly valid. Instead
of strsplit, I use regexpr to find only the *first* occurrence of an
equals sign, and then I use substr to extract the part of the tag
before and after the equals sign. The attached file is a patch against
"R/gff.R" in the rtracklayer dist. I developed the patch against
version 1.16.1.

Regards,

-Ryan Thompson