appliedbinf / URDO-SMOREd

Sequence Matching fOr REpiratory Diseases, SMORE'D, is a command-line sequence classification tool tailored to meet the needs of the Undiagnosed Respiratory Disease Outbreak (URDO) branch at CDC. SMORE'D is a k-mer based classification tool capable of rapidly classifying read sequences generated by multi-pathogen detection platforms.

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Resistance kmers #15

Open ar0ch opened 4 years ago

ar0ch commented 4 years ago

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
[x] Convert user input kmers to REGEX
[ ] Add two-pass classification for read processor

ar0ch commented 4 years ago

16 Tracking code additions

ar0ch commented 4 years ago

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