evol rankorder


Running evol rankorder -h displays:

usage: evol rankorder [-h] [--quiet] [--examples] [-z] [-d STR] [-p STR]
                      [-m STR] [-l STR] [-n INT] [-q INT] [-t FLOAT] [-u]
                      [-o STR]

positional arguments:
  mutinfo               mutual information matrix

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

input options:
  -z, --zscore          apply zscore for identifying top ranked coevolving
  -d STR, --delimiter STR
                        delimiter used in mutual information matrix file
  -p STR, --pdb STR     PDB file that contains same number of residues as the
                        mutual information matrix, output residue numbers will
                        be based on PDB file
  -m STR, --msa STR     MSA file used for building the mutual info matrix,
                        output residue numbers will be based on the most
                        complete sequence in MSA if a PDB file or sequence
                        label is not specified
  -l STR, --label STR   label in MSA file for output residue numbers

output options:
  -n INT, --num-pairs INT
                        number of top ranking residue pairs to list (default:
  -q INT, --seq-sep INT
                        report coevolution for residue pairs that are
                        sequentially separated by input value (default: 3)
  -t FLOAT, --min-dist FLOAT
                        report coevolution for residue pairs whose CA atoms
                        are spatially separated by at least the input value,
                        used when a PDB file is given and --use-dist is true
                        (default: 10.0)
  -u, --use-dist        use structural separation to report coevolving pairs
  -o STR, --outname STR
                        output filename, default is mutinfo_rankorder.txt


Running evol rankorder --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