pick_otus_through_otu_table.py
Description:
This script takes a sequence file and performs all processing steps through building the OTU table.
Usage: pick_otus_through_otu_table.py [options]
Input Arguments:
Note
[REQUIRED]
- -i, --input_fp
The input fasta file [REQUIRED]
- -o, --output_dir
The output directory [REQUIRED]
[OPTIONAL]
- -p, --parameter_fp
Path to the parameter file, which specifies changes to the default behavior. See http://www.qiime.org/documentation/file_formats.html#qiime-parameters . [if omitted, default values will be used]
- -f, --force
Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: None]
- -w, --print_only
Print the commands but don't call them -- useful for debugging [default: False]
- -a, --parallel
Run in parallel where available [default: False]
- -O, --jobs_to_start
Number of jobs to start. NOTE: you must also pass -a to run in parallel, this defines the number of jobs to be started if and only if -a is passed [default: 4]
Output:
This script will produce an OTU mapping file (pick_otus.py), a representative set of sequences (FASTA file from pick_rep_set.py), a sequence alignment file (FASTA file from align_seqs.py), taxonomy assignment file (from assign_taxonomy.py), a filtered sequence alignment (from filter_alignment.py), a phylogenetic tree (Newick file from make_phylogeny.py) and a biom-formatted OTU table (from make_otu_table.py).
Simple example:
The following command will start an analysis on seqs.fna (-i), which is a post-split_libraries fasta file. The sequence identifiers in this file should be of the form <sample_id>_<unique_seq_id>. The following steps, corresponding to the preliminary data preparation, are applied: Pick de novo OTUs at 97%; pick a representative sequence for each OTU (the OTU centroid sequence); align the representative set with PyNAST; assign taxonomy with RDP classifier; filter the alignment prior to tree building - remove positions which are all gaps, and specified as 0 in the lanemask; build a phylogenetic tree with FastTree; build an OTU table. All output files will be written to the directory specified by -o, and subdirectories as appropriate. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).
pick_otus_through_otu_table.py -i $PWD/seqs.fna -o $PWD/otus/