Get gene calls and their sequences from an anvi'o contigs database

get_genes.py

from anvio.dbops import ContigsSuperclass

# if your args object contains a `contigs_db` entry in its
# namespace all you don't need the following two lines and
# you can directly pass it to the ContigsSuperclass.
import argparse
args = argparse.Namespace(contigs_db="INFANT-GUT-TUTORIAL/SPLITAH/E_facealis/CONTIGS.db")

# get an instance of the contigs super:
contigs_db = ContigsSuperclass(args)

# learn every gene caller in the database:
gene_caller_ids = list(contigs_db.genes_in_contigs_dict.keys())

# and you're done:
gene_caller_ids, gene_sequences_dict = contigs_db.get_sequences_for_gene_callers_ids(gene_caller_ids, include_aa_sequences=True)

# how many genes?
print(f"num genes:\n{len(gene_caller_ids)}\n\n")

# first few gene caller ids:
print(f"first few gene caller ids:\n{gene_caller_ids[0:20]}\n\n")

# just to see the output data structure, lets
# print out the very first entry in gene sequences
# dict :)
print(f"example data for gene caller id 17:\n")
import anvio
anvio.P(gene_sequences_dict[4])

terminal_oputput.txt

$ python get_genes.py

num genes:
2754


first few gene caller ids:
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]


example data for gene caller id 17:

{
  "sequence": "ATGAAACATTCACAACTTGTGGCGATTATTAAGAGACTGGAAGCAATGATCGAAGCAGCAGATAATGAAGTACAAGTACGCCGCTTTGAACGTGAAGGCGTAGAGAAATGTATTGTAAGTTTTGATAAATCAACAGAAACATTTGAATTAACAGAATCTGATACGCACCAAAGCTATCAATTCGATAACATCGATATTGTAGCAATGGAAATTTACGACTTAATTCAATAA",
  "contig": "Day17a_QCcontig1",
  "start": 3552,
  "stop": 3783,
  "direction": "f",
  "rev_compd": "False",
  "length": 231,
  "aa_sequence": "MKHSQLVAIIKRLEAMIEAADNEVQVRRFEREGVEKCIVSFDKSTETFELTESDTHQSYQFDNIDIVAMEIYDLIQ"
}