amplicons_histograms.py – Create histograms of predicted amplicons for primer pairs

Description:

Using amplicons files (generated with get_amplicons_and_reads.py), this module will generate histogram(s) showing the predicted amplicon sizes. If a taxonomy mapping file is passed, the histograms will be separated according to domain (archaea, bacteria, and eukaryotic).

Usage: amplicons_histograms.py [options]

Input Arguments:

Note

[REQUIRED]

-f, --amplicons_filepath

Target amplicons files. Separate multiple files with a colon.

[OPTIONAL]

-o, --output_dir

Specify output directory for amplicons and reads. [default: .]

-r, --all_files

Generate histograms for all files ending with _amplicons.fasta in the directory specified with the -f parameter [default: False]

-t, --taxa_map

Filepath to taxonomy mapping file, used to separate graphs according to domain. [default: None]

Output:

There will be an output graph in postscript format with the same root name as the input _amplicons.fasta file for each _amplicons.fasta file passed.

Standard Example usage (create a histogram from an amplicon file, output to the current directory):

amplicons_histograms.py [options] {-f amplicons_filepath }

Test for all _amplicons.fasta files in current directory, pass a taxonomy mapping file so histograms are plotted according to domain, and output to amplicons_graph directory:

amplicons_histograms.py -f . -r -t taxonomy_mapping.txt -o amplicons_graph