Analyze the Results (#2)

• Now, that we have run cliffy. Let's analyze the *.listings file output by cliffy to give concrete classifications for each read.

• In order to analyze the output, use the analyze_doclisting.py script in the analysis/ folder.

  • --mate-1: path to mate1.listings file generated from cliffy
  • --mate-2: path to mate2.listings file generated from cliffy
  • --doc-id-to-taxa: a text file mapping each document id to a SILVA taxa
  • --silva-taxa-names: a text file summarizing the ranks for each SILVA taxa
  • --output-file: path for output file, where each read will be classified.
  • --read-level: tells cliffy to output classifications at the read-level
  • --abundance-profile: tells cliffy to output genera level abundances

# generate per-read classifications
python3 analyze_cliffy.py analyze --mate-1 cliffy_tutorial/example2_query/mate1.listings 
                                  --mate-2 cliffy_tutorial/example2_query/mate2.listings 
                                  --doc-id-to-taxa cliffy_tuturial/example2_data/doc_to_traversal.txt 
                                  --silva-taxa-names cliffy_tutorial/example2_data/tax_slv_ssu_138.1.txt 
                                  --output-file cliffy_tutorial/example2_query/read_classifications.cliffy 
                                   --read-level

# generate abundance profile
python3 analyze_cliffy.py analyze --mate-1 cliffy_tutorial/example2_query/mate1.listings 
                                  --mate-2 cliffy_tutorial/example2_query/mate2.listings 
                                  --doc-id-to-taxa cliffy_tuturial/example2_data/doc_to_traversal.txt 
                                  --silva-taxa-names cliffy_tutorial/example2_data/tax_slv_ssu_138.1.txt 
                                  --output-file cliffy_tutorial/example2_query/abundance_profiles.cliffy 
                                  --abundance-profile

• These commands will generate two output files:
  • per-read classifications: can be found at cliffy_tutorial/example2_query/read_classifications.cliffy
  • abundance profiles: can be found at cliffy_tutorial/example2_query/read_classifications.cliffy