Joshua Orvis

Home from my conference and travels. Will get to these tickets later today, just FYI.

I have tracked down this issue. The problem is with the library's treatment of genes with multiple isoforms. When it sees more than one mRNA for a particular gene, it's...

As a side note, we should evaluate this with what this does: http://www.ncbi.nlm.nih.gov/pubmed/22962361

Thanks for submitting this. You're right, that implementation's documentation is a good starting point, though it allows a lot of room for expansion. It doesn't check anything about encoding conventions...

The basic classes are now added, but nothing to iterate over them yet.

Here is an example implementation which could serve as the starting point to improve upon: https://github.com/jorvis/biocode/blob/master/fastq/fastq_simple_stats.py

This is fixed with this pull request (if it gets accepted): https://github.com/DmitryUlyanov/Multicore-TSNE/pull/92

This is fixed with this pull request (if it gets accepted): https://github.com/DmitryUlyanov/Multicore-TSNE/pull/92

It doesn't work for me either and I don't even get a console error.

I'm getting this issue still with 2.3.4 when doing a download of a public profile. It seems to only happen when I pass the -T option. If I leave that...