ydeng/bch441-work-abc-units
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Update - file locations and authorization of phylip apps on Mac.

Browse Source
This commit is contained in:
hyginn 2020-09-26 18:21:17 +10:00
parent 85b7353646
commit b9ac373fce
1 changed files with 28 additions and 10 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

38
BIN-PHYLO-Tree_building.R
View File

@ -1,11 +1,5 @@
# tocID <- "BIN-PHYLO-Tree_building.R"
#
# ---------------------------------------------------------------------------- #
# PATIENCE ... #
# Do not yet work wih this code. Updates in progress. Thank you. #
# boris.steipe@utoronto.ca #
# ---------------------------------------------------------------------------- #
#
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-PHYLO-Tree_building unit.
#
@ -15,7 +9,8 @@
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 1.2 deprecate save()/load() for saveRDS()/readRDS()
# 1.2 deprecate save()/load() for saveRDS()/readRDS(); Mac:
# instructions to authorize proml.app
# 1.1 Change from require() to requireNamespace(),
# use <package>::<function>() idiom throughout,
# 1.0 First 2017 version
@ -86,6 +81,23 @@ if (! requireNamespace("Rphylip", quietly = TRUE)) {
# directly to that subdirectory to find the program it needs:
# PROMLPATH <- "/Applications/phylip-3.695/exe/proml.app/Contents/MacOS"
# However, RPHYLIP will not be able to run PHYLIP applications immediately,
# because they have not been "signed" by the PHYLIP developers. The process
# will terminate by your system, with a warning.
# - Navigate to the phylip folder in your ~/Applications directory
# - Descend into the "exe" folder and find proml.app
# - Ctrl-click proml.app and choose "Open". A dialogue will show that
# says: "macOS cannot verify the developer of “proml.app”.
# Are you sure you want to open it?"
# - Click open to continue. You may need to allow access to the terminal
# as well. When the proml terminal session open, you can type
# Ctrl-c to abort the program and close the window.
#
# This adds proml.app to the list of known-good programs and you will not
# need to repeat this process.
#
# === 1.1.2 ... on Windows
# On Windows you need to know where the programs have been installed, and you
# need to specify a path that is correct for the Windows OS. Find the folder
@ -114,11 +126,17 @@ list.files(PROMLPATH) # lists the files [1] "proml" "proml.command"
# If "proml" is NOT among the files that the last command returns, you
# can't continue. Ask on the mailing list for advice.
# If everything is good, you can add the line that defines PROMLPATH to
# myScripts/.myProfile.R - the path will then be automatically set when
# you quit RStudio and return.
# == 1.2 Building a maximum likelihood tree ================================
# Now read the mfa file you have saved in the BIB-PHYLO-Data_preparation unit,
# as a "proseq" object with the read.protein() function of the RPhylip package:
apsIn <- Rphylip::read.protein("APSESphyloSet.mfa")
apsIn <- Rphylip::read.protein("data/APSESphyloSet.mfa")
str(apsIn)
# ... and you are ready to build a tree.
@ -130,7 +148,7 @@ apsIn <- Rphylip::read.protein("APSESphyloSet.mfa")
# as you can throw at it. Calculating a tree of 48 APSES domains
# with default parameters of Rproml() runs for more than half a day
# on my computer. But we have only twelve sequences here, so the
# process will take us about 5 to 10 minutes. Run this, and anjoy a good cup
# process will take us about 5 to 15 minutes. Run this, and anjoy a good cup
# of coffee while you are waiting.
apsTree <- Rphylip::Rproml(apsIn, path=PROMLPATH)
@ -140,7 +158,7 @@ apsTree <- Rphylip::Rproml(apsIn, path=PROMLPATH)
plot(apsTree)
# save your tree:
saveRDS(apsTree, file = "APSEStreeRproml.rds")
saveRDS(apsTree, file = "data/APSEStreeRproml.rds")
# If this did not work, ask for advice.