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liaoherui / StrainScan

High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01615-w
MIT License
32 stars 4 forks source link

updated build_tree code #5

Open nick-youngblut opened 1 year ago

nick-youngblut commented 1 year ago

Switched to os.path.join and os.makedirs for paths. Switched to f" " and sys.stderr.write for string formatting and writing updates to the console.

@liaoherui you may want to consider using codon to speed up at least some of the python functions in build_tree and other parts of the codebase.

liaoherui commented 1 year ago

Thanks! I will check the codes and merge them! Also, appreciate for the suggestions about using "codon". I will see whether I can use it to speed up the program!