RUN_TIPP.PY(1)

📦 version 1.0, in ubuntu jammy

💖 RUN_TIPP.PY(1) — bestie edition 💖

okay so you found run_tipp.py, section 1 of the manual (User Commands, iykyk), and honestly? she's a lot, but she's worth it. let's get into it 🫶

✨ NAME ✨

run_tipp.py — an identification and phylogenetic profiling tool 🌸

✨ DESCRIPTION ✨

here's the whole usage vibe, verbatim, because I'm not about to paraphrase a synopsis:

usage: run_tipp.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] [-R N] [-at N] [-D] [-pt N] [-PD N] [-tx TAXONOMY]
       [-txm MAPPING] [-adt TREE] [-C N]

so like, what does she do? This script runs the SEPP algorithm on an input tree, alignment, fragment file, and RAxML info file. periodt. 💅

she needs a reference dataset though, and you have to download it from:

https://obj.umiacs.umd.edu/tipp/tipp2-refpkg.tar.gz

now listen — if your local administrator has not set the path to this reference dataset in /etc/tipp/tipp.config, then you gotta copy that file over to ~/.tipp/ and drop the path to the dataset into the reference section of the configuration file. go read tipp.config(5), she explains it better than me. 🎀

🌈 optional arguments:

  • -h, --help — show this help message and exit. the classic. iconic. 🫶
  • -v, --version — show program's version number and exit. ✨

🧚 DECOMPOSITION OPTIONS:

these options determine the alignment decomposition size and taxon insertion size. If None is given, then the default is to align/place at 10% of total taxa. and important bestie: the alignment decomosition size must be less than the taxon insertion size. no negotiating. 💀

  • -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 controlling memory. [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 output. yes she's got a whole section for it. main character energy fr fr.

  • -p DIR, --tempdir DIR — Tempfile files will be written to DIR. Full-path required. [default: /tmp/sepp]
  • -rt, --remtemp — Remove template directory. [default: disabled]
  • -o OUTPUT, --output OUTPUT — output files with prefix OUTPUT. [default: output]
  • -d OUTPUT_DIR, --outdir OUTPUT_DIR — output to OUTPUT_DIR directory. full-path required. [default: .]

🦋 INPUT OPTIONS:

these options control input. To run SEPP the following is required: 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. and heads up: the input sequences are assumed to be DNA unless specified otherwise. 💜

  • -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 machinery section, bestie. 🔥

  • -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. slay.

  • -R N, --reference_pkg N — Use a pre-computed reference package [default: None]
  • -at N, --alignmentThreshold N — Enough alignment subsets are selected to reach a commulative probability of N. This should be a number between 0 and 1 [default: 0.95]
  • -D, --dist — Treat fragments as distribution
  • -pt N, --placementThreshold N — Enough placements are selected to reach a commulative probability of N. This should be a number between 0 and 1 [default: 0.95]
  • -PD N, --push_down N — Whether to classify based on children below or above insertion point. [default: True]
  • -tx TAXONOMY, --taxonomy TAXONOMY — A file describing the taxonomy. This is a commaseparated text file that has the following fields: taxon_id,parent_id,taxon_name,rank. If there are other columns, they are ignored. The first line is also ignored.
  • -txm MAPPING, --taxonomyNameMapping MAPPING — A comma-separated text file mapping alignment sequence names to taxonomic ids. Formats (each line): sequence_name,taxon_id. If there are other columns, they are ignored. The first line is also ignored.
  • -adt TREE, --alignmentDecompositionTree TREE — A newick tree file used for decomposing taxa into alignment subsets. [default: the backbone tree]
  • -C N, --cutoff N — Placement probability requirement to count toward the distribution. This should be a number between 0 and 1 [default: 0.0]

💅 SEE ALSO 💅

go read those too, they're part of the lore 📚✨

okay that's the whole page!! this one's from run_tipp.py, September 2021, and it lives in the RUN_TIPP.PY(1) section of the manual. go forth and phylogenetically profile, bestie — you got this 💖🦋🌸🎀🫶

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