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nielshanson edited this page Sep 13, 2013 · 22 revisions

Welcome to the Wiki for the utilities repo. Here we've put some documentation and examples on how to use some of the analytical scripts.

NCBI Submssion

generate_ncbi_gss.py: A script to create .gss and the parallel .pub, .lib, and .cont files from .fasta files containing environmental fosmid-end sequences for submission to dbGSS. For more information see the official dbGSS website at the NCBI.
gss_to_fasta.py: A script to create .fasta files from .gss files.

Analysis

calculate_4mer_freq.py: A script to calculate the tetra-nucleotide (4-mer) frequency from a set of .fasta files, creating a matrix of all 256 4-mers as a tab-delimited file --- ready for loading into R.

Data Base Preparation

prepare_gg.py: The GreenGenes 16s rRNA database has been updated (May 2013) and has a new home on the web. However, the format of the database has changed as it no longer comes with a .fasta file that is ammenable to BLAST database creation. This script combines the available taxonomy, genbank, and sequence references to construct such a file.