Step 3: BioCyc Processing

Step 3.1: Extract BioCyc Data

# Extract BioCyc database files
tar -xvzf biocyc-flatfiles.tar.gz -C /path/to/Biocyc

# Create a list of all organism directories with full paths
readlink -f Biocyc/* > directory.list

Step 3.2: Process Per-Species Database Files

For each BioCyc organism database, extract enzyme-reaction, EC number, reaction, and Pfam information.

Expected output: One *_RXNS.txt file per species
Columns: RXN, EC_NUMBERS, PFAM, uniref90_ids

for CURRENT_DIR in $(cat directory.list); do
    echo "Processing: $CURRENT_DIR"
    bash get_rxns.sh $CURRENT_DIR OUTPUT_DIR
done

For large BioCyc releases, this can be parallelised as a SLURM array job — one task per organism directory.

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Next: Step 4 — Mapping RXNs to Gene Families