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RUN_TIPP.PY(1) User Commands RUN_TIPP.PY(1)

NAME

run_tipp.py - an identification and phylogenetic profiling tool

DESCRIPTION

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]

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

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

optional arguments:

show this help message and exit
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.
max alignment subset size of N [default: 10% of the total number of taxa or the placement subset size if given]
max placement subset size of N [default: 10% of the total number of taxa or the alignment length (whichever bigger)]
maximum fragment chunk size of N. Helps controlling memory. [default: 20000]
minimum p-distance before stopping the decomposition[default: 1]
maximum tree diameter before stopping the decomposition[default: None]
decomposition strategy [default: using tree branch length]

OUTPUT OPTIONS:

These options control output.
Tempfile files will be written to DIR. Full-path required. [default: /tmp/sepp]
Remove template directory. [default: disabled]
output files with prefix OUTPUT. [default: output]
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.
A config file, including options used to run SEPP. Options provided as command line arguments overwrite config file values for those options. [default: None]
Input tree file (newick format) [default: None]
RAxML_info file including model parameters, generated by RAxML.[default: None]
Aligned fasta file [default: None]
fragment file [default: None]
Molecule type of sequences. Can be amino, dna, or rna [default: dna]
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
Use N cpus [default: number of cpus available on the machine]
checkpoint file [default: no checkpointing]
Interval (in seconds) between checkpoint writes. Has effect only with -cp provided. [default: 3600]
random seed number. [default: 297834]

TIPP OPTIONS:

These arguments set settings specific to TIPP
Use a pre-computed reference package [default: None]
Enough alignment subsets are selected to reach a commulative probability of N. This should be a number between 0 and 1 [default: 0.95]
Treat fragments as distribution
Enough placements are selected to reach a commulative probability of N. This should be a number between 0 and 1 [default: 0.95]
Whether to classify based on children below or above insertion point. [default: True]
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.
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.
A newick tree file used for decomposing taxa into alignment subsets. [default: the backbone tree]
Placement probability requirement to count toward the distribution. This should be a number between 0 and 1 [default: 0.0]

SEE ALSO

run_sepp.py(1), tipp.config(5)

September 2021 run_tipp.py