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sstevens_pubscrip

This repo contains scripts written by Sarah Stevens.

For more but poorly documented scripts see my other script repo

parse_phylosift_sts.py

This script is meant to be used on the sequence_taxa_summary file output from the program PhyloSift run on a single genome or genome bin. It goes though each linnean classification level and removes any marker gene hits below the set cutoffprob. value. It then looks for a classification matching above the cutoffperc. value specified.

filterbylen3.py

This script takes a fasta file and filters out reads/contigs which are below your minlen cutoff.

maskrRNAgbk.py

This script takes a genbank file and replaces any nucleotides annotated as rRNA with N's. Written for python3. Outputs a fasta file.