Ensemble Enzyme Prediction Pipeline (E2P2)

The Ensemble Enzyme Prediction Pipeline (E2P2) annotates protein sequences with Enzyme Function classes comprised of full, four-part Enzyme Commission numbers and MetaCyc reaction identifiers. It is the enzyme annotation pipeline used to generate the species-specific metabolic databases at the Plant Metabolic Network since 2013. E2P2 systematically integrates results from two molecular function annotation algorithms using an ensemble classification scheme. For a given genome, all protein sequences are submitted as individual queries against the base-level annotation methods.

Getting Started

The following instuctions are for users to set up the E2P2 pipeline on a Unix machine and start running, developing and/or testing the pipeline.

Prerequisites

This pipeline is tested on Ubuntu, CentOS, macOS and should theoretically run on all Linux distributions.

• Python 3
• NCBI BLAST+
• Java 1.5 or above
• PRIAM_Search utility V2

Installing

Download E2P2 from E2P2 at GitHub

git clone https://github.com/carnegie/E2P2.git

Download Reference Protein Sequence Dataset (RPSD) from https://ftp.dpb.carnegiescience.edu/rpsd/

Unzip and extract RPSD data

tar -xzf blastdb.tar.gz
tar -xzf profiles.tar.gz
tar -xzf weights.tar.gz
tar -xzf maps.tar.gz

# If you want to just use the required arguments with a different version of RPSD data, 
# replace the "maps" and "weights" folders under "data" in "E2P2" using the above folders 
# with the same name.

Usage Example

python3 run_pipeline.py [-h] --input /PATH/TO/Araport11_genes.201606.pep.repr.fasta --blastp blastp --java java --priam_search /PATH/TO/PRIAM_search.jar --rpsd /PATH/TO/blastdb/rpsd-4.2.fasta --priam_profile /PATH/TO/profiles

Required Arguments

--input INPUT_FILE, -i INPUT_FILE: Path to input protein sequences file

--blastp BLASTP_CMD, -b BLASTP_CMD: Command of or path to NCBI BLAST+ "blastp" executable.

--java JAVA_CMD, -j JAVA_CMD: Command of or path to "java" executable.

--priam_search PRIAM_SEARCH, -ps PRIAM_SEARCH: Path to "PRIAM_search.jar" executable.

--rpsd RPSD_DB, -r RPSD_DB: Path to RPSD BLAST database name.
  For example, "/PATH/TO/FOLDER/rpsd.fa", where you can find the following files in /PATH/TO/FOLDER: rpsd.fa.phr; rpsd.fa.pin; rpsd.fa.psq
  
--priam_profile PRIAM_PROFILE, -pp PRIAM_PROFILE: Path to PRIAM profiles.
  For example, "/PATH/TO/FOLDER/profiles", where you can find the following in /PATH/TO/FOLDER/profiles:
    files: annotation_rules.xml; genome_rules.xml
    folder: PROFILES: this contains a "LIBRARY" folder and multiple ".chk" files.

Optional Arguments

-h, --help: Show help message and exit

--output OUTPUT_PATH, -o OUTPUT_PATH: Path to output file. By Default it would be in the same folder of the input.

--num_threads NUM_THREADS, -n NUM_THREADS: Number of threads to run "blastp". Default is 1

--priam_resume, -pr: Whether or not to resume process if a unfinished PRIAM_search.jar process is found.

--blast_bin BLAST_BIN, -bb BLAST_BIN: Command of or path to NCBI BLAST+ bin folder. By Default, the pipeline would try to retrieve the path from the '--blastp/-b' input path.

--blast_weight BLAST_WEIGHT, -bw BLAST_WEIGHT: Path to weight file for the blast classifier. By default, the path would be defined in the 'definitions' module

--blast_evalue EVALUE, -be EVALUE: blastp evalue cutoff. Default is 1e-2

--priam_weight PRIAM_WEIGHT, -pw PRIAM_WEIGHT: Path to blast weight for the priam classifier

--efmap EF_MAP, -e EF_MAP: Path to Enzyme function class to Metacyc RXN-ID/EC Number file (efclasses.mapping).

--threshold THRESHOLD, -th THRESHOLD: Threshold for voting results. Default is 0.5.

--temp_folder TEMP_FOLDER, -tf TEMP_FOLDER: Specify the location of the temp folder that contains classifier results. By default it would be in the same directory of the output.

--log LOG_PATH, -l LOG_PATH: Specify the location of the log file. By default it would be "runE2P2.log" in the temp folder.

--protein_gene PROTEIN_GENE_PATH, -pg PROTEIN_GENE_PATH: Provide a protein to gene mapping file. This will be used to generate a splice variant removed fasta file and output our final version of e2p2.

--verbose {0,1}, -v {0,1}: Verbose level of log output. Default is 0.
   0: only step information are logged
   1: all information are logged

Additional information

• Input protein sequences should be in FASTA format.
• Headers of the FASTA file should begin with the sequence ID followed by a space or '|'. For example: >AT1G01010.1 | NAC domain containing protein 1 | Chr1:3760-5630 FORWARD LENGTH=429 | 201606

Authors

• Bo Xue - bxuecarnegie

Previous versions

• Chuan Wang - Chuan Wang
• Lee Chae

Institution

Plant Metabolic Network
Department of Plant Biology
Carnegie Institution for Science
Stanford, CA 94305

Acknowledgments

• Special Thanks to
  • Thomas Bernard - PRIAM