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

Resistance kmers #15

Open
1 of 5 tasks
ar0ch opened this issue Aug 21, 2019 · 2 comments
Open
1 of 5 tasks

Resistance kmers #15

ar0ch opened this issue Aug 21, 2019 · 2 comments
Assignees
Labels
enhancement New feature or request

Comments

@ar0ch
Copy link
Member

ar0ch commented Aug 21, 2019

The following functionality needs to be added:

  • Standardize naming scheme and file form for resistance kmer "db" file
  • New section to configuration file for resistance kmer file
  • Update config loading function for resistance kmer section
  • Convert user input kmers to REGEX
  • Add two-pass classification for read processor
@ar0ch ar0ch added the enhancement New feature or request label Aug 21, 2019
@ar0ch ar0ch added this to the SMOREd 1.0 milestone Aug 21, 2019
@ar0ch
Copy link
Member Author

ar0ch commented Aug 21, 2019

#16 Tracking code additions

@ar0ch
Copy link
Member Author

ar0ch commented Aug 22, 2019

Proposed definition:

>header
NNNATGNNN

Where header is a heading matching the characterization column, N's are any base that get transformed into the REGEX [ATCG]{1} and ATG is the codon of interest. Multiple codons may be represented in the string, e.g. NNNGAANNNNNNATA

@ar0ch ar0ch removed this from the SMOREd 1.0 milestone Jan 28, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

2 participants