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chrisquince / DESMAN

De novo Extraction of Strains from MetAgeNomes
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Python2 vs python3 #48

Open tstraub89 opened 3 years ago

tstraub89 commented 3 years ago

It seems like DESMAN is now written in python3, but the Snakemake tutorial that creates a py2 and py3 environment does not reflect this update.

chrisquince commented 3 years ago

Hi Tim,

The snakmake is out of date. We have most of its components in various other projects:

Analysing MAGs https://github.com/chrisquince/STRONG

Start from a single genome https://github.com/chrisquince/DESMANSnake

If you let me know what you want to do, I can put the relevant snake on the Desman repo?

Thanks, Chris

tstraub89 commented 3 years ago

Hey Chris,

Thanks for your quick reply. My goal is to resolve multiple E. coli strains from metagenomic assemblies of multiple, related samples. I would like to be able to separate out which contigs, genes, and/or variants belong to distinct strains within the given set of samples. Any suggestions would be much appreciated!

Thanks, Tim

chrisquince commented 3 years ago

Hi Tim,

Desman can definitely do this, but it sounds like your starting point is individual sample assemblies not one coassembly? Individual sample assemblies will make the sample mapping challenging but it may work. Do you have your entire E coli genome in each sample binned out successfully?

Alternatively my suggestion might be that your start with a coassembly. Then you need to identify the E coli bins. In fact you need the snakemake in this repo which as I mentioned needs serious updating. I could try and find the time to do that later on this week?

Thanks, Chris

tstraub89 commented 3 years ago

Hey Chris,

I appreciate the offer!

I have slowly (but surely) gotten the Desman snakemake pipline to work on my end. Essentially I put everything except the steps that rely on CONCOCT code on to the py3 environment and installed all the dependencies into the py3 environment as well. I then edited the rules file to activate the py2 environment only for those steps.

I'm still testing it and am currently running the Desman step. Once I can verify my changes work all the way through, I'll be happy to share my rules.snake file.

Tim

chrisquince commented 3 years ago

Hi Tim,

Sounds good! I would be very keen to look at the snake and with your permission we can either replace the one in the repo or use yours to correct it? I will instead use my time to update the doc a bit.

Best, Chris

marcomeola commented 3 years ago

Any update here?