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.

: 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]

-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: .]

: 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]

-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]

-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]