mdc_compare.py

Compare residue-residue contact frequencies from different files by generating a comparison plot and table

usage: mdc_compare_neighborhoods.py [-h] [-a ANCHOR] [-k KEYS] [-c COLORS] [-m MUTATIONS] [-t TITLE] [-p] [-o OUTPUT_DESC] [-gx GRAPHIC_EXT] files [files ...]

Positional Arguments

files

R|Files (ASCII or .xlsx) containing the frequencies and labels in the first two or three columns. Minimal examples could be : >>> #freq label >>> 1. GLU30-ALA50 >>> .75 ALA50-ASP40 or >>> 1. GLU30 ALA50 >>> .75 ALA50 ASP40 Lines startint with ‘#’ are ignored

Named Arguments

-a, --anchor

A residue that appears in all contacts. It will be eliminated from the labels for clarity.

-k, --keys

The keys used to label the files, e.g. ‘WT,MUT’

-c, --colors

Colors to use for the dicts, defaults to “tab:blue, tab:orange, tab:green, tab:red, tab:purple, tab:brown, tab:pink, tab:gray, tab:olive, tab:cyan”

Default: “tab:blue,tab:orange,tab:green,tab:red,tab:purple,tab:brown,tab:pink,tab:gray,tab:olive,tab:cyan”

-m, --mutations

A replacement dictionary, to be able to re-label residues across systems, e.g. “GLU:ARG,LYS:PHE” changes all GLUs to ARGs and all LYS to PHEs

-t, --title

Title of the plot. Default is “comparison”

Default: “comparison”

-p, --pop-up

pop-up an interactive figure before closing. Default is not to pop-up but directly save to file

Default: False

-o, --output_desc

Descriptor for output files. Default is freq_comparison

Default: “freq_comparison”

-gx, --graphic_ext

Extension of the output graphics, default is .pdf

Default: “.pdf”