CAZy_utils

Utilities for parsing CAZy GI numbers, and creating blastDB compatible fasta files and MetaCyc functional hierarchies. Assumes the use of an sqlite database to create hierarchy.

Contents:

download_cazy_pages.py: A simple script to download CAZy HTML pages from http://www.cazy.org/. Uses the structure of their URL to download all the HTML tables from each family. load_cazy_db.py: Script parses HTML tables files downloaded with download_cazy_pages.py to export

Example Use

This procedure worked at time of writing, but I antisipate that it may have to be re-factored slightly if the CAZy HTML format or NCBI API changes.

Downloaded CAZy HTML files with download_cazy_pages.py

python download_cazy_pages.py

Note: You may want to check the families dictionary to make sure there are no new CAZy families added.

Load SQLITE database of CAZy information

• parse HTML files and load into the SQLite database

python load_cazy_db.py -i *html --db CAZY_SQLITE_DB

where,

• -i: is a glob of the CAZy HTML tables downloaded in the previous step
• --db: path to the CAZY_SQLITE_DB

Note: The script currently assume the SQLite database contains a table of the form:

CREATE TABLE `CAZY_2014_09_04` (
	`fam`	TEXT,
	`num`	TEXT,
	`super`	TEXT,
	`org`	TEXT,
	`protein`	TEXT,
	`ec`	TEXT,
	`genbank`	TEXT,
	`uniprot`	TEXT,
	`pdb`	TEXT,
	`subf`	TEXT
);

Download RefSeq Sequences using the NCBI Web API

• refseq_seqs_from_db pulls all the unique NCBI GI numbers from the SQLite and pulls from from the Web API in batches of 500
• Produces a FASTA file compatible with the CAZy hierarchy for MetaPathways
• Note: A stable internet connection is critical here

python refseq_seqs_from_db.py --db <SQLITE_DB> -t <DB_ TABLE_NAME> -o <OUTPUT_FILE>

Extract CAZy Hierarchy for MetaPathways

• extract CAZy functional hierarchy for MetaPathways from the SQLite database

python extract_cazy_hierarchy_from_db.py --db <SQLITE_DB> -t <DB_ TABLE_NAME> -o <OUTPUT_FILE>