Category Archives: Phage

Submitting a PhiSpy update to pip and conda

First, make sure everything is upto date in GitHub.

We are going to call this release version 4.0 and we will have release candidates, starting at rc1

First, create a release on GitHub. Strictly speaking you don’t need to do that but it is a great thing to do.

PyPi Release

The PyPi instructions cover this, but I have abstracted out the parts we need to focus on (since we have a setup.py already!) Lets start by ensuring we are upto date (note that I do this as root)

pip3 install --upgrade setuptools wheel

As a regular user we switch back to the PhiSpy directory and build everything. This make a new release that we will upload

python3 setup.py sdist

This will create the tarball and the wheel file in the dist directory. Then we need to upload those to PyPi.

We are going to use the PyPi test interface to make sure that everything is OK. Do not skip this step!

If you need an API key, navigate to the PyPi login page . However, if you have done this before, you probably don’t need to save it again đŸ˜‰

python3 -m twine upload --repository testpypi dist/PhiSpy-4.0.0rc1.tar.gz

Note that you can not upload the wheel. Binary wheels from linux are not supported.

Now we are going to test it out. Lets make a virtual environment and install it there

virtualenv test_phispy
cd test_phispy
source bin/activate
which pip

This should tell you that the current pip is from your virtual environment. If it is not, solve that problem!

For PhiSpy, we have a couple of dependencies that you should install with regular pip before you can install your new release candidate:

pip3 install scikit-learn biopython

This will install other things like numpy that you need.

Now you can install your new release.

pip install -i https://test.pypi.org/simple/ PhiSpy==4.0.0rc1

If you are not sure exactly the URL, logging into the PyPi test login page will show your available repositories, including the newly uploaded repository. If you click on the version you want, you can get the link to download and install that.

Once you are happy and have run some tests, login to the real PyPi page (good to do anyway, even if you have an API key)

Now you can upload the final version to PyPi for everyone to access

python3 -m twine upload dist/PhiSpy-4.0.0.tar.gz

Its worth logging into the real PyPi page to make sure that you can download it!

Making a CONDA release

It turns out that for PhiSpy all you have to do is wait! The conda bots will take care of incrementing to the next version and running the continuous integration tests for you.

Press about Global Phylogeography of crAssphage

Our paper on the global phylogeography of crAssphage is published in Nature Microbiology. You can read the paper at the Nature Microbiology website or on ReadCube. The paper garnered international press attention, and here we have summarized the press coverage.

Please let Rob know if you are aware of any other reports that are not included here.

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crAssphage poops up again!

Yet again, analysis of a metagenomic sample shows that crAssphage is the most abundant phage anywhere. It also shows what a dis-service NCBI did to science by deleting the crAssphage record. We used meta-spades to reconstruct the entire crAssphage genome from someone else’s data set, but in their paper, the largest contig was ~3 kb. This analysis suggests that crAssphage is present in ulcerative colitis samples but the abundance goes down after treatment!

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Phage Identification

We are interested in phages — viruses that infect bacteria. For years the Edwards’ lab has been looking at new, undiscovered phages.

Recently, we identified the crAssphage, a new type of virus that has never been seen before. By looking at the sequences in metagenomes we were able to identify a set of contigs that were common among many different metagenomes. When we assembled them, they looked like a phage. We could compare them to other known phages in our database of sequences.

Working with folks in the biology department we proved that this is a circular virus by using PCR. However, we have so far been unable to culture the virus in vivo. We’re working on it, and hopefully others are too, but until that point we don’t have an image of the virus or an idea of what it does.