NAME
run_abundance.py - helper script to estimate the abundance at a given taxonomic level
DESCRIPTION
usage: run_abundance.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] [-at N] [-pt N] [-g N] [-b N] [-bin N] [-D] [-C N] [-G GENES]
This script runs the SEPP algorithm on an input tree, alignment, fragment file, and RAxML info file.
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
- -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]
- -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]
- -g N, --gene N
-
Classify on only the specified gene.
- -b N, --blast_file N
-
Blast file with fragments already binned.
- -bin N, --bin_using N
-
Tool for binning
- -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]