run_abundance.py1
Helper script to estimate the abundance at a given taxonomic level
Overview
usage: run_abundance.py [-h] [-v] [-A N] [-P N] [-F N] [--distance DISTANCE]
- [-M DIAMETER] [-S DECOMP] [-p DIR] [-o OUTPUT]
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[-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
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-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.
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-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]
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-P N, --placementSize N -
max placement subset size of N [default: 10% of the total number of taxa or the alignment length (whichever bigger)]
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-F N, --fragmentChunkSize N -
maximum fragment chunk size of N. Helps controlling memory. [default: 20000]
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--distance DISTANCE -
minimum p-distance before stopping the decomposition[default: 1]
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-M DIAMETER, --diameter DIAMETER -
maximum tree diameter before stopping the decomposition[default: None]
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-S DECOMP, --decomp_strategy DECOMP -
decomposition strategy [default: using tree branch length]
Output options:
-
These options control output.
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-p DIR, --tempdir DIR -
Tempfile files will be written to DIR. Full-path required. [default: /tmp/sepp]
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-o OUTPUT, --output OUTPUT -
output files with prefix OUTPUT. [default: output]
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-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.
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-t TREE, --tree TREE -
Input tree file (newick format) [default: None]
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-r RAXML, --raxml RAXML -
RAxML_info file including model parameters, generated by RAxML.[default: None]
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-a ALIGN, --alignment ALIGN -
Aligned fasta file [default: None]
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-f FRAG, --fragment FRAG -
fragment file [default: None]
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-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
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-x N, --cpu N -
Use N cpus [default: number of cpus available on the machine]
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-cp CHCK_FILE, --checkpoint CHCK_FILE -
checkpoint file [default: no checkpointing]
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-cpi N, --interval N -
Interval (in seconds) between checkpoint writes. Has effect only with
-cpprovided. [default: 3600]
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-seed N, --randomseed N -
random seed number. [default: 297834]
Tipp options:
-
These arguments set settings specific to TIPP
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-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]
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-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]
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-g N, --gene N -
Classify on only the specified gene.
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-b N, --blast_file N -
Blast file with fragments already binned.
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-bin N, --bin_using N -
Tool for binning
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-D, --dist -
Treat fragments as distribution
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-C N, --cutoff N -
Placement probability requirement to count toward the distribution. This should be a number between 0 and 1 [default: 0.0]
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-G GENES, --genes GENES -
Use markers or cogs genes [default: markers]