Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Seq2struct #54

Open
wants to merge 17 commits into
base: main
Choose a base branch
from
Open

Seq2struct #54

wants to merge 17 commits into from

Conversation

jmbilodeaux
Copy link
Collaborator

approach to map tRNA structure position to sequence position anchoring nanopore sequence space to structure of tRNA.

Mapping file is created using test.py. Needs to be edited to include the "uncharged" 3' adapter sequence and language to distinguish the two tRNAs in reference file.

test data is charged seq of WT ecoli infected or not with T4

"""Reads a FASTA file (gzipped or plain) and returns sequences and headers."""
ref_sequences, ref_headers = {}, []

with open(file_name, 'rt') as file:
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Use Bio.SeqIO for this?

@jayhesselberth
Copy link
Member

jayhesselberth commented Mar 10, 2025

We should think about where to put these files. A new seq2struct directory is probably not the place. This pipeline is built on the recommended snakemake structure:

https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#distribution-and-reproducibility

You should reorganize with that in mind. I am guessing resources/s2s might be an option.

You should also document all of this somewhere, maybe in the README.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants