Applications.py using a deprecated method from Bio
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
Comments (5)
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reporter Thank you Jason, for the fix and for the awesome tool that you share with the community!
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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.
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- changed status to resolved
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. -
reporter Thank you very much, Jason!
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Thanks for reporting this, Ariel. I’ve pushed fix for this issue to the repo using
SeqIO.write()
withformat="fasta-2line"
to replicate the zero line wrap output provided bySeqIO.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).