Applications.py using a deprecated method from Bio

[Ariel Erijman]

In makeBlastnDB, SeqIO.FastaIO.FastaWriter is deprecated and is not working in a new conda environment with only presto and it’s dependencies.

I made it work by replacing

writer = SeqIO.FastaIO.FastaWriter(seq_handle, wrap=None)
writer.write_file(ref_dict.values())```  

for

SeqIO.write(ref_dict.values(), seq_handle,  format="fasta")

I would appreciate if you could make that fix and update conda as I need it for our pipeline in nextflow.

Thank you,

Ariel

[Jason Vander Heiden]

Thanks for reporting this, Ariel. I’ve pushed fix for this issue to the repo using SeqIO.write() with format="fasta-2line" to replicate the zero line wrap output provided by SeqIO.FastaIO.FastaWriter.

This means we had to increase in the Biopython dependency version, so tests are running now (we need to make sure the immcantation docker container still builds and such). We should be able to push a new version to PyPI after all that’s done (I assume the conda install will work after it’s on PyPI).

[Ariel Erijman]

Thank you Jason, for the fix and for the awesome tool that you share with the community!

[Jason Vander Heiden]

Sure thing. Glad it’s of use!

Docker test build went fine. I have a couple little things to check still, but I’ll try to do the release tomorrow.

[Jason Vander Heiden]

I pushed presto v0.6.1 to PyPI with this fix. Please reopen if you have any issues with it.

If you're using the Immcantantion docker container, it might take a few days before this is included. There's a bug in alakazam::groupGenes we need to do a release for, so we're going to wait on that.

[Ariel Erijman]

Thank you very much, Jason!