In this tutorial we will showcase how a restez database
can be used to speed up a phylotaR run.
phylotaR runs an automated pipeline for identifying
orthologous gene clusters as the first step in a phylogenetic analysis.
A user provides a taxonomic identity and the pipeline downloads all
relevant sequences and identifies clusters using a local-alignment
search tool. For more information on phylotaR see its published article.
By using restez in conjunction with
phylotaR, we will not only being saving time, but also
improving the chances of a successful phylotaR run – often
NCBI Entrez limits the number of requests or even rejects requests from
IP addresses that are making too many. Note, however, that the gains in
using restez with phylotaR only make sense if
you make use of the restez database multiple times or if
you wish to radically increase the maximum number of sequences to
download per taxon (by default it is only 3,000). Also, note that using
a restez database does not currently eliminate the need for
an internet connection. phylotaR still needs to look up
taxonomic information and must also identify relevant sequence IDs using
Entrez (this may change in the future as restez
develops).
We will run a phylotaR run for the rodent subfamily,
Dipodinae, the clade that contains jerboas. Because this clade is so
small, it should not take too long to run it. We will, however, limit to
showcasing only the download stage of the phylotaR
pipeline, where restez is required.
Install phylotaR
# Currently only the development version of phylotaR can work with restez
# It must be installed from GitHub using devtools
devtools::install_github(repo = 'ropensci/phylotaR')Setup
Since we will be running the phylotaR pipeline for
Dipodinae, we can use the rodents database we created before.
We do not need to set-up the phylotaR pipeline any
differently with a restez database, except to ensure we
have set the restez path to the rodent database.
library(phylotaR)
# Restez (no need to call package)
restez::restez_path_set(filepath = rodents_path)
# Vars
wd <- 'dipodinae'
dir.create(wd)
txid <- 35737 # Dipodinae
mxsql <- 500
ncbi_dr <- '[PATH/TO/BLAST]' # e.g. '/usr/local/ncbi/blast/bin'
# setup
setup(wd = wd, txid = txid, ncbi_dr = ncbi_dr, mxsql = 500)Run
# run just the first two stages for this demonstration
taxise_run(wd)
#> ---------------------------------------------------
#> Starting stage TAXISE: [2023-07-24 07:00:06.361265]
#> ---------------------------------------------------
#> Searching taxonomic IDs ...
#> Downloading taxonomic records ...
#> . [1-38]
#> Generating taxonomic dictionary ...
#> ---------------------------------------------------
#> Completed stage TAXISE: [2023-07-24 07:00:09.45394]
#> ---------------------------------------------------
download_run(wd)
#> -----------------------------------------------------
#> Starting stage DOWNLOAD: [2023-07-24 07:00:09.456996]
#> -----------------------------------------------------
#> Identifying suitable clades ...
#> Identified [1] suitable clades.
#> Connecting to restez database ...
#> Downloading hierarchically ...
#> Working on parent [id 35737]: [1/1] ...
#> . + whole subtree ...
#> . . Getting [300 sqs] from restez database...
#> Successfully retrieved [300 sqs] in total.
#> ------------------------------------------------------
#> Completed stage DOWNLOAD: [2023-07-24 07:00:16.345238]
#> ------------------------------------------------------Sequences that cannot be found locally will be downloaded via Entrez.
Sequences may not be found locally for three sets of reasons, 1.
phylotaR may have identified non-GenBank sequences
(e.g. RefSeq), 2. the local database may have size limits (ours has a
min of 100 and a max 1000), and 3. the local database is out of date,
new GenBank releases are only made once a month.
Note: If the
phylotaRmessages do not explicit state that they are using arestezdatabase, then, you may not have set therestezpath.
Compared to running without a restez database, phylotaR
download can run 2x
faster.