Category Archives: Lab blog

minimap2 hints

Here are some tips and tricks for minimap2 that I keep forgetting!

–split-prefix

If you have a large (>4 GB) multisequence index file, there are two options.

The first is to increase the value of -I when you build the index (preferred) so that the whole index is kept in memory. Note: This must be done when you build the index, you can’t build the index and then change -I during runtime.

The second is to use --split-prefix with a string. For snakemake, there are two options:

  1. You can use "{sample}" as your prefix like so:
params:
    prfx = "{sample}"
...
shell:
    """
         minimap2 --split-prefix {params.prfx} ...
    """

2. You can use a random 6 character string like so:

import random, string

params:
        pfx = ''.join(random.choices(string.ascii_uppercase + string.digits, k=6)) 
...
shell:
    """
         minimap2 --split-prefix {params.prfx} ...
    """

The trick is here, things will probably break if your index file is small. If you see the errorr: [W::sam_hdr_create] Duplicated sequence it is probably because you have split a small index sequence, and the sequence IDs are being duplicated. Remove the --split-prefix option and you should be good.

Primer Trimming Challenge

In DNA sequencing, we add primers and adapters to the ends of sequences. These are short (typically <50bp) known sequences, that we use so we can identify different kinds of sequences. You can find out more about the adapters in this YouTube video.

This challenge is to write software to efficiently detect and remove the primers and adapters from a fastq format file.

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Global Distribution of Crassphage Map

How to make beautiful maps

Making maps is hard. Even though we’ve been making maps for hundreds of years, it is still hard. Making good looking maps is really hard. We published a map that is both beautiful and tells a story, and this is the story of how we made that map.

But a figure like this does not appear immediately, it takes work to get something to look this good, and needless to say it wasn’t me that made it look so great!

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Django logo

Publishing a Django Website behind a proxy server

We use proxy servers all the time: we have a main server (eg http://edwards.sdsu.edu/) that serves applications (eg. http://edwards.sdsu.edu/GenomePeek) but the application itself runs on different hardware than the webserver.

Here, we show how to host a Django project on a proxy server using the apache web server and make it accessible.

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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!)

As a regular user we 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 😉

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 most code 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.

However, if you need to update the code manually, you probably need to change the version in meta.yaml and then you should update the SHA hash:

wget -O- https://github.com/linsalrob/PhiSpy/archive/v4.1.16.tar.gz | shasum -a 256

and then paste the output of that into the SHA field. In this case, the shasum should be

1d3579e83125d4ccf108d2e369a4c56984d12f1c8ff483d90efaf99cb6182d44