mdu-phl / lissero Goto Github PK

Create a recipe for Bioconda.

Here are some docs: https://bioconda.github.io/contributor/guidelines.html

Here is the emmtyper recipe as a model: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/emmtyper/meta.yaml

You will need to start by forking the Bioconda repo https://github.com/bioconda/, and creating a new branch (lissero).

One you finished creating and testing the recipe, make sure to squash your commits (git rebase -i master) - here is a good instruction set to keep handy: https://github.com/wprig/wprig/wiki/How-to-squash-commits, and then you can to the PR request to the main Bioconda repo. @tseemann can help.

I have create the following table to show how LisSero interprets a certain combination of amplicons, compared to the paper of Doumith. As you can see, LisSero assigns the serotype to a lot of combinations that do not appear in the Doumith paper. I was wondering if this classification is documented somewhere, is it from another publication?

Hi Jason.

When printing multiple elements that are in a field separated by commas, there should be no space between the comma and the record. That makes parsing the output a bit of a nightmare.

So:

1/2b, 3b, 7

Should be:

1/2b,3b,7

So, the whole line looks like this:

contigs.fa   1/2b,3b,7     ORF2819,Prs

Anders.

If you download the file from github you must make modifications in lines: 13,14,15. We should delete lissero.

in line 16 delete the . in init.

Hi Anders,

There seems to have some issue with BlastN...

When I tried to run the job, it looks like the failing bit is at this step.

$ lissero test.fna
2021-07-14 12:01:45.731 | INFO     | lissero.scripts.Serotype:_load_log:285 - Successfully loaded DB log!
2021-07-14 12:01:45.731 | INFO     | lissero.scripts.Serotype:check_db:260 - DB was created on 2020-06-04T11:57:55.145347
2021-07-14 12:01:45.731 | INFO     | lissero.scripts.Serotype:check_db:261 - DB is ready for use.
2021-07-14 12:01:45.732 | INFO     | lissero.scripts.Sample:get_serotype:29 - Serotyping: test.fna
2021-07-14 12:01:45.732 | INFO     | lissero.scripts.Blast:run:52 - Blastn is running: /home/users/iidlleo/miniconda3/envs/phetype/bin/blastn -db /home/users/iidlleo/miniconda3/envs/phetype/lib/python3.6/site-packages/lissero/db/lissero -ungapped -culling_limit 1 -outfmt 6 qaccver saccver length slen pident -dust no -query /scratch/iidlleo/eyre/test.fna
2021-07-14 12:01:45.743 | CRITICAL | lissero.scripts.Blast:run:55 - Failed to run /home/users/iidlleo/miniconda3/envs/phetype/bin/blastn -db /home/users/iidlleo/miniconda3/envs/phetype/lib/python3.6/site-packages/lissero/db/lissero -ungapped -culling_limit 1 -outfmt 6 qaccver saccver length slen pident -dust no -query /scratch/iidlleo/eyre/test.fna

I am using blast v2.5.0, and I could found the dbs if list the directory

$ ls /home/users/iidlleo/miniconda3/envs/phetype/lib/python3.6/site-packages/lissero/db/
lissero_db.json  lissero.nhr  lissero.nog  lissero.not  lissero.ntf  sequences.fasta
lissero.ndb      lissero.nin  lissero.nos  lissero.nsq  lissero.nto

This is caused by missing setuptools in a brand new environment.

Should migrate to importlib.resources--- but it would mean we would have to set python 3.7 as minimum requirement.

In the meantime, need to add setuptools to dependency to ensure proper installation from conda.

when I run the command (in terminal not conda enviroment) python3 run_lissero.py I get the following error:

_Traceback (most recent call last):

File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 349, in get_provider
module = sys.modules[moduleOrReq]
KeyError: 'lissero'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/chris_franco/bin/programas_bioinformaticos/LisSero/lissero/run_lissero.py", line 20, in
DEFAULT_DB = pkg_resources.resource_filename("lissero", "db")
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 1135, in resource_filename
return get_provider(package_or_requirement).get_resource_filename(
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 351, in get_provider
import(moduleOrReq)
ModuleNotFoundError: No module named 'lissero'

do yu have any suggetion for fix them.

Requirements:

• The software should be open source as per the OSI definition.
• The software should have an obvious research application.
• You should be a major contributor to the software you are submitting.
• The software should be a significant contribution to the available open source software that either enables some new research challenges to be addressed or makes addressing research challenges significantly better (e.g., faster, easier, simpler).
• The software should be feature-complete (no half-baked solutions) and designed for maintainable extension (not one-off modifications). Minor ‘utility’ packages, including ‘thin’ API clients, and single-function packages are not acceptable.
• Your paper (paper.md and BibTeX files, plus any figures) must be hosted in a Git-based repository. Placing these items together with your software (rather than in a separate repository) is strongly encouraged.

Your paper should include:

• A list of the authors of the software and their affiliations, using the correct format (see the example below).
• A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience.
• A clear Statement of Need that illustrates the research purpose of the software.
• A list of key references, including to other software addressing related needs.
• Mention (if applicable) a representative set of past or ongoing research projects using the software and recent scholarly publications enabled by it.
• Acknowledgement of any financial support.

Example paper: https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography

Create a Using GitHub Action called validation.yml that will run the tool against all the validation genomes, and assert we get the right results.

I would add the assemblies into the repo (but we don't package them) to validations/data/<assembler_version>/<sample_id>/contigs.fa folder in the root folder.

Then add a csv with the expected results in validations/data/pcr-results.csv.

It will then need a small NextFlow pipeline that runs the latest lissero on the controls, and on each of the genomes.

It then compares the output of lissero with the expected output to assert they are the same.

I believe @kristyhoran has a template of what the validation report might look like, so the NextFlow pipeline would ideally output that in PDF. The plain text version of the filled in template (before conversion to PDF) would be committed to validations/reports/ along with a CSV of the raw data (i.e., the one row per sample with the sample ID, the expected result, the observed result, and whether they match or not.

The NextFlow pipeline should be in validations/validation.nf and the config file should be validations/config.nextflow.

I appreciate there is a lot to this issue. I would start with just getting the NextFlow pipeline working on a local clone of the repo, and then work towards getting it working with the GitHub Actions.

Fails on blast 2.5
please make lissero check blast -version before running.
And add to docs

Pasteur is curating FASTA with various alleles of the Listeria serogroups.

https://bigsdb.pasteur.fr/api/db/pubmlst_listeria_seqdef/schemes/4

http://emboss.sourceforge.net/download/

maybe was just an outage at sf.net ?

Dear Jason,

First of all, congratulations for LisSero. It will be a very useful tool!!!

I am trying to install it on a Unix environment, but the link provided in the HELP file regarding the download of EMBOSS PrimerSearch is not working...(and consequently, the LIsSero doesn't run!)

I would like to kindly ask you if you could provide us the correct link, or another alternative to install PrimerSearch.

I am looking forward to testting LisSero!!!

Best regards,

Vítor Borges

We need the following three flags added to the tool before we can publish:

1. --positive-control
2. --negative-control
3. --controls

The first one should runs a positive control, which can be the EGDE-e strain (https://www.ncbi.nlm.nih.gov/assembly/GCF_000196035.1/)

The second one runs two negative controls Listeria innocua Clip11262 strain (https://www.ncbi.nlm.nih.gov/assembly/GCF_000195795.1/) and Salmonella enterica subsp Typhimurium LT2 strain (https://www.ncbi.nlm.nih.gov/assembly/GCF_000006945.2).

Download these genomes, and add them to the repo to be part of the packaged data.

When the user uses the --positive-control flag it will run the EGDE-e strain, and it should assert that the result is correct before going forward (I believe it is 1/2a), or gracefully exit with an error.

When the user adds the --negative-control flag it will return both the Listerian innocua and Salmonella enterica genomes both as Nontypeable. That particular Listeria innocua strain lacks the Prs gene. It should assert we get the expected values before going forward, or gracefully exit with an error.

The options --controls runs both --postive-control and --negative-control.