run_tipp.py1

An identification and phylogenetic profiling tool

Overview

usage: run_tipp.py [-h] [-v] [-A N] [-P N] [-F N] [--distance DISTANCE]

: [-M DIAMETER] [-S DECOMP] [-p DIR] [-o OUTPUT] [-d OUTPUT_DIR] [-t TREE] [-r RAXML] [-a ALIGN] [-f FRAG] [-m MOLECULE] [-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]

This script runs the SEPP algorithm on an input tree, alignment, fragment file, and RAxML info file. It uses a reference dataset which has to be downloaded from https://github.com/tandyw/tipp-reference/releases/download/v2.0.0/tipp.zip

If the local administrator has not set the path to this reference dataset in /etc/sepp/tipp.config, you should copy this file to ~/.sepp/ and put the path to the dataset in the reference section of the configuration file, see tipp.config(5).

optional arguments:

-h, --help: show this help message and exit

-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. The alignment decomosition size must be less than the taxon insertion size.

-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.

-p DIR, --tempdir DIR: Tempfile files will be written to DIR. Full-path required. [default: /tmp/sepp]

-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. The input sequences are assumed to be DNA unless specified otherwise.

-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]

Other options:

: These options control how SEPP is run

-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

-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]