-
Notifications
You must be signed in to change notification settings - Fork 1
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
base: main
Are you sure you want to change the base?
Seq2struct #54
Conversation
seq2struct/test.py
Outdated
"""Reads a FASTA file (gzipped or plain) and returns sequences and headers.""" | ||
ref_sequences, ref_headers = {}, [] | ||
|
||
with open(file_name, 'rt') as file: |
There was a problem hiding this comment.
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?
We should think about where to put these files. A new You should reorganize with that in mind. I am guessing You should also document all of this somewhere, maybe in the README. |
…ion to reference position
…rather than Rfam tRNA cm model
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