Closed FelixErnst closed 4 years ago
I met the same problem. I found the following changes of GenomicRanges in their NEWS. Hopefully, it is useful for debugging.
...
DEPRECATED AND DEFUNCT
o Deprecate several RangedData methods: seqinfo, seqinfo<-, seqnames, and
findOverlaps#RangedData#GenomicRanges
RangedData objects will be deprecated in BioC 3.9 (their use has been
discouraged since BioC 2.12, that is, since 2014). Package developers
that are still using RangedData objects need to migrate their code to
use GRanges or GRangesList objects instead.
BUG FIXES
o Make [[, as.list(), lapply(), and unlist() fail more graciously on
a GenomicRanges object.
o Make "show" methods for GenomicRanges and GPos objects robust to
special metadata column names like "stringsAsFactors".
o Export the "update" method for GRanges objects. This addresses
https://github.com/Bioconductor/GenomicRanges/issues/7
Hi @gmbecker
any chance this might get fixed?
I will get this fixed today or tomorrow. Thanks
On Wed, Mar 18, 2020 at 2:44 AM Felix Ernst notifications@github.com wrote:
Hi @gmbecker https://github.com/gmbecker
any chance this might get fixed?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/gmbecker/genbankr/issues/4#issuecomment-600521591, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAG53MLDGBG6K7KSHQM4ZT3RICJZJANCNFSM4GXYAU4Q .
Well that didn't happen, apologies. I have pushed a potential fix to the Bioconductor git repos (in master, ie devel) as package version 1.15.2. Please give it a try when you get the chance and make sure the output iso coorrect.
BTW, the issue stemmed from the transcript_id annotation being missing for the exons, which may (or may not?) be an error/oversight in the genbank file.
Hope this works and sorry again for the long delay.
Thanks for the fix. I didn't have the chance to test it, since the changes are not found in this repo, are they?
Regarding the version number: Do you mean 1.15.2? 1.15 is the current Bioc devel version and you cannot go down.
@FelixErnst yes, 1.15.2, sorry. And the package should be available in the devel repo in the next day or two.
The fixed work. Regarding the missing transcript_id: I think that the special nature of the accession number (It is human rRNA) might also play a role. However, now genbankr is the only solution I found so far, to retrieve rRNA information in the Bioconductor universe. TxDb doesn't contain it and ensembl is also weird and inconsistent.
Thank you, @gmbecker.
I will close this.
Hi
The following call ends up with an error originating from the GenomicRanges packages.
I am not sure, what might be the problem, but it seams that the GenomicRanges packages is used in an incompatible way.