Running :command:`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
Running :command:`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