evol refine


Running evol refine -h displays:

usage: evol refine [-h] [--quiet] [--examples] [-l STR] [-s FLOAT] [-c FLOAT]
                   [-r FLOAT] [-k] [-o STR] [-f STR] [-z]

positional arguments:
  msa                   MSA filename to be refined

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

refinement options:
  -l STR, --label STR   sequence label, UniProt ID code, or PDB and chain
  -s FLOAT, --seqid FLOAT
                        identity threshold for selecting unique sequences
  -c FLOAT, --colocc FLOAT
                        column (residue position) occupancy
  -r FLOAT, --rowocc FLOAT
                        row (sequence) occupancy
  -k, --keep            keep columns corresponding to residues not resolved in
                        PDB structure, applies label argument is a PDB

output options:
  -o STR, --outname STR
                        output filename, default is msa filename with _refined
  -f STR, --format STR  output MSA file format, default is same as input
  -z, --compressed      gzip refined MSA output


Running evol refine --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