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rjones-scripts

This repository contains utility scripts written by Robert E. Jones

Scripts

  • gc_filter.py - Plots (histogram) and filters genome contigs based on gc content.

    • Usage: python3 gc_filter.py [--filter FILTER] [--plot] in_file out_dir

  • rename_proteome_contigs.py - Takes a directory of proteomes (with .faa extensions) as input. Outputs proteomes with renamed headers (UniqueID_g<N>) and a key tsv file containing the new headers and the original headers.

    • Usage: python3 rename_proteome_contigs.py in_dir out_dir

  • replicate_missing_data.py - Replicates missing data in a simulated matrix.

    • Usage: python3 real_infile sim_infile out_file

  • sequence_reformat.py - Reformats requence files.

    • Usage: python3 sequence_reformat.py in_file in_format out_file out_format

  • web_blast.py - BLAST against an online database (nr, nt, swissprot, etc.) using blastn, blastp, blastx, tblastn, or tblastx.

    • Usage: python3 -u get_mito_genome.py -q QUERY -d DATABASE -b BLAST_TYPE