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Analyze the Results (#2)
Omar Ahmed edited this page Jul 26, 2024
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3 revisions
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Now, that we have run
cliffy
. Let's analyze the*.listings
file output bycliffy
to give concrete classifications for each read. -
In order to analyze the output, use the
analyze_doclisting.py
script in theanalysis/
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
: tellscliffy
to output classifications at the read-level -
--abundance-profile
: tellscliffy
to output genera level abundances
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# 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:
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per-read classifications
: can be found atcliffy_tutorial/example2_query/read_classifications.cliffy
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abundance profiles
: can be found atcliffy_tutorial/example2_query/read_classifications.cliffy
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