evol fetch

Usage

Running evol fetch -h displays:

usage: evol fetch [-h] [--quiet] [--examples] [-a STR] [-f STR] [-o STR]
                  [-i STR] [-g STR] [-t INT] [-d PATH] [-p STR] [-z]
                  acc

positional arguments:
  acc                   Pfam accession or ID

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

download options:
  -a STR, --alignment STR
                        alignment type, one of full, seed, ncbi, metagenomics
                        (default: full)
  -f STR, --format STR  Pfam supported MSA format, one of selex, fasta,
                        stockholm (default: selex)
  -o STR, --order STR   ordering of sequences, one of tree, alphabetical
                        (default: tree)
  -i STR, --inserts STR
                        letter case for inserts, one of upper, lower (default:
                        upper)
  -g STR, --gaps STR    gap character, one of dashes, dots, mixed (default:
                        dashes)
  -t INT, --timeout INT
                        timeout for blocking connection attempts (default: 60)

output options:
  -d PATH, --outdir PATH
                        output directory (default: .)
  -p STR, --outname STR
                        output filename, default is accession and alignment
                        type
  -z, --compressed      gzip downloaded MSA file

Examples

Running evol fetch --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