RUN_ABUNDANCE.PY(1)

💖 RUN_ABUNDANCE.PY — the girlies' guide 💖

okay so bestie, this is a page from User Commands (section 1 of the manual), and it's all about run_abundance.py. Buckle up, we're learning a helper script and we're gonna slay it 🎀

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✨ NAME ✨

run_abundance.py — a helper script that estimates the abundance at a given taxonomic level. that's it, that's the vibe 🦋

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🌸 DESCRIPTION 🌸

here's the usage, no cap, exactly as written:

usage: run_abundance.py [-h] [-v] [-A N] [-P N] [-F N] [--distance DISTANCE]
       [-M DIAMETER] [-S DECOMP] [-p DIR] [-rt] [-o OUTPUT]
              [-d OUTPUT_DIR] [-c CONFIG] [-t TREE] [-r RAXML] [-a ALIGN] [-f
              FRAG] [-m MOLECULE] [--ignore-overlap] [-x N] [-cp CHCK_FILE]
              [-cpi N] [-seed N] [-bt N] [-at N] [-pt N] [-g N] [-b N]
              [-no_trim] [-bin N] [-D] [-C N] [-G GENES]

so basically: this script runs the SEPP algorithm on an input tree, alignment, fragment file, and RAxML info file. main character energy fr fr 👑

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💅 OPTIONS 💅

🫶 optional arguments:

• -h, --help — shows this help message and dips. iconic behavior.
• -v, --version — shows the program's version number and exits. short king.

🧚 DECOMPOSITION OPTIONS:

these options decide the alignment decomposition size and the taxon insertion size. if None is given, the default is to align/place at 10% of total taxa. and heads up bestie — the alignment decomposition size must be less than the taxon insertion size. no exceptions, that's the rule 💀

• -A N, --alignmentSize N — max alignment subset size of N [default: 10% of the total number of taxa or the placement subset size if given]
• -P N, --placementSize N — max placement subset size of N [default: 10% of the total number of taxa or the alignment length (whichever bigger)]
• -F N, --fragmentChunkSize N — maximum fragment chunk size of N. helps control memory. she's practical 💅 [default: 20000]
• --distance DISTANCE — minimum p-distance before stopping the decomposition [default: 1]
• -M DIAMETER, --diameter DIAMETER — maximum tree diameter before stopping the decomposition [default: None]
• -S DECOMP, --decomp_strategy DECOMP — decomposition strategy [default: using tree branch length]

🌈 OUTPUT OPTIONS:

these options control the output. where the girlies' files go 🎀

• -p DIR, --tempdir DIR — tempfile files will be written to DIR. full-path required. [default: /tmp/sepp]
• -rt, --remtemp — remove the tempfile directory. clean up after yourself, queen ✨ [default: disabled]
• -o OUTPUT, --output OUTPUT — output files with prefix OUTPUT. [default: output]
• -d OUTPUT_DIR, --outdir OUTPUT_DIR — output to the OUTPUT_DIR directory. full-path required. [default: .]

🔥 INPUT OPTIONS:

these control the input. to run SEPP you need the following, periodt. a backbone tree (in newick format), a RAxML_info file (this is the file generated by RAxML during estimation of the backbone tree — pplacer uses this info file to set model parameters), a backbone alignment file (in fasta format), and a fasta file including fragments. the input sequences are assumed to be DNA unless specified otherwise. iykyk 🧬

• -c CONFIG, --config CONFIG — a config file, including options used to run SEPP. options provided as command line arguments overwrite config file values for those options. [default: None]
• -t TREE, --tree TREE — input tree file (newick format) [default: None]
• -r RAXML, --raxml RAXML — RAxML_info file including model parameters, generated by RAxML. [default: None]
• -a ALIGN, --alignment ALIGN — aligned fasta file [default: None]
• -f FRAG, --fragment FRAG — fragment file [default: None]
• -m MOLECULE, --molecule MOLECULE — molecule type of sequences. can be amino, dna, or rna [default: dna]
• --ignore-overlap — when a query sequence has the same name as a backbone sequence, ignore the query sequences and keep the backbone sequence [default: False]

💜 OTHER OPTIONS:

these options control how SEPP is run. the mechanics, the logistics, the behind-the-scenes 🦋

• -x N, --cpu N — use N cpus [default: number of cpus available on the machine]
• -cp CHCK_FILE, --checkpoint CHCK_FILE — checkpoint file [default: no checkpointing]
• -cpi N, --interval N — interval (in seconds) between checkpoint writes. has effect only with -cp provided. [default: 3600]
• -seed N, --randomseed N — random seed number. [default: 297834]

🌟 TIPP OPTIONS:

these arguments set settings specific to TIPP. the special-est settings 🎀

• -bt N, --blastThreshold N — minimum query coverage for blast hit to map read to a marker. this should be a number between >0 [default : 50]
• -at N, --alignmentThreshold N — enough alignment subsets are selected to reach a cumulative probability of N. this should be a number between 0 and 1 [default: 0.95]
• -pt N, --placementThreshold N — enough placements are selected to reach a cumulative probability of N. this should be a number between 0 and 1 [default: 0.95]
• -g N, --gene N — classify on only the specified gene.
• -b N, --blast_file N — blast file with fragments already binned.
• -no_trim, --do_not_trim_after_blast — trim query sequence if it extends outside marker (BLAST only).
• -bin N, --bin_using N — use blast or hmmer for binning [default: blast]
• -D, --dist — treat fragments as distribution
• -C N, --cutoff N — placement probability requirement to count toward the distribution. this should be a number between 0 and 1 [default: 0.0]
• -G GENES, --genes GENES — use markers or cogs genes [default: markers-v3]

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👑 SEE ALSO 👑

run_sepp.py(1), run_tipp.py(1),

go read those too, bestie, they're part of the family 💖

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okay that's the whole page!! this one's from the run_abundance.py page, September 2021 edition — sending u all the love, stay hydrated, and remember: the alignment decomposition size must be less than the taxon insertion size 💅✨🫶