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.. _evol-fetch:
evol fetch
====================
Usage
--------------------
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
Examples
--------------------
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
|
