evol occupancy


Running evol occupancy -h displays:

usage: evol occupancy [-h] [--quiet] [--examples] [-o STR] [-p STR] [-l STR]
                      [-f STR] [-S] [-X STR] [-Y STR] [-T STR] [-D INT]
                      [-W FLOAT] [-F STR] [-H FLOAT]

positional arguments:
  msa                   MSA file

optional arguments:
  -h, --help            show this help message and exit
  --quiet               suppress info messages to stderr
  --examples            show usage examples and exit

calculation options:
  -o STR, --occ-axis STR
                        calculate row or column occupancy or both., one of
                        row, col, both (default: row)

output options:
  -p STR, --prefix STR  output filename prefix, default is msa filename with
                        _occupancy suffix
  -l STR, --label STR   index for column based on msa label
  -f STR, --number-format STR
                        number output format (default: %12g)

figure options:
  -S, --save-plot       save occupancy plot/s
  -X STR, --xlabel STR  specify xlabel
  -Y STR, --ylabel STR  specify ylabel
  -T STR, --title STR   figure title
  -D INT, --dpi INT     figure resolution (dpi) (default: 300)
  -W FLOAT, --width FLOAT
                        figure width (inch) (default: 8)
  -F STR, --figure-format STR
                        figure file format, one of png, pdf, raw, svg, eps,
                        ps, svgz, rgba (default: pdf)
  -H FLOAT, --height FLOAT
                        figure height (inch) (default: 6)


Running evol occupancy --examples displays:

Sequence coevolution analysis involves several steps that including
retrieving data and refining it for calculations.  These steps are
illustrated below for RnaseA protein family.

Search Pfam database:

  $  evol search 2w5i

Download Pfam MSA file:

  $  evol fetch RnaseA

Refine MSA file:

  $ evol refine RnaseA_full.slx -l RNAS1_BOVIN --seqid 0.98 --rowocc 0.8

Checking occupancy:

  $ evol occupancy RnaseA_full.slx -l RNAS1_BOVIN -o col -S

Conservation analysis:

  $ evol conserv RnaseA_full_refined.slx

Coevolution analysis:

  $ evol coevol RnaseA_full_refined.slx -S -c apc

Rank order analysis:

  $ evol rankorder RnaseA_full_refined_mutinfo_corr_apc.txt -p 2w5i_1-121.pdb --seq-sep 3