evol filter


Running evol filter -h displays:

usage: evol filter [-h] [--quiet] [--examples] (-s | -e | -c) [-F] [-o STR]
                   [-f STR] [-z]
                   msa word [word ...]

positional arguments:
  msa                   MSA filename to be filtered
  word                  word to be compared to sequence label

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

filtering method (required):
  -s, --startswith      sequence label starts with given words
  -e, --endswith        sequence label ends with given words
  -c, --contains        sequence label contains with given words

filter option:
  -F, --full-label      compare full label with word(s)

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 filter --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