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Maintance: typos, update of prosite URL

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hyginn 2018-12-02 18:52:36 +10:00
parent 1dd87e7473
commit 2ab162e375
4 changed files with 13 additions and 12 deletions
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2
BIN-PHYLO-Tree_building.R
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@ -79,7 +79,7 @@ if (!require(Rphylip, quietly=TRUE)) {
# PROMLPATH <- "/Applications/phylip-3.695/exe/proml.app/Contents/MacOS" # PROMLPATH <- "/Applications/phylip-3.695/exe/proml.app/Contents/MacOS"
# === 1.1.2 ... on Windows # === 1.1.2 ... on Windows
# On Windows you need to know where the rograms have been installed, and you # 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 # need to specify a path that is correct for the Windows OS. Find the folder
# that is named "exe", and right-click to inspect its properties. The path # that is named "exe", and right-click to inspect its properties. The path
# should be listed among them. # should be listed among them.

8
BIN-Storing_data.R
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@ -180,9 +180,9 @@ autoincrement <- function(table) {
autoincrement(philDB$person) autoincrement(philDB$person)
# Once that is clear, let's remove the Zhuangzi entry and recreate it correctly. # Once that is clear, let's remove the Zhuangzi entry and recreate it correctly.
# Many ways to remove, here we use a logical expression to select matching record(s), # Many ways to remove, here we use a logical expression to select matching
# apply the results to subset the data frame, and overwrite the existing table # record(s), apply the results to subset the data frame, and overwrite the
# with the new one. # existing table with the new one.
sel <- !(philDB$person$name == "Zhuangzi") # select ... sel <- !(philDB$person$name == "Zhuangzi") # select ...
philDB$person <- philDB$person[sel, ] # ... and replace philDB$person <- philDB$person[sel, ] # ... and replace
@ -260,7 +260,7 @@ philDB$books$title
sel <- numeric() # initialize the vector sel <- numeric() # initialize the vector
for (ID in pID) { for (ID in pID) {
sel <- which(philDB$works$personID == ID) # get all rows for which sel <- which(philDB$works$personID == ID) # get all rows for which
# the condition is TRUE # the condition is TRUE
cat(sprintf("%s: ", philDB$person$name[ID])) # output the person cat(sprintf("%s: ", philDB$person$name[ID])) # output the person
cat(sprintf("\"%s\" ", philDB$books$title[sel])) # output the book cat(sprintf("\"%s\" ", philDB$books$title[sel])) # output the book
cat("\n") cat("\n")

9
RPR-PROSITE_POST.R
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@ -3,12 +3,13 @@
# Purpose: A Bioinformatics Course: # Purpose: A Bioinformatics Course:
# R code accompanying the RPR-Scripting_data_downloads unit. # R code accompanying the RPR-Scripting_data_downloads unit.
# #
# Version: 1.0 # Version: 1.0.1
# #
# Date: 2017 10 05 # Date: 2017 10 - 2018 12
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 1.0.1 Updates for slightly changed interfaces
# 1.0 First ABC units version # 1.0 First ABC units version
# 0.1 First code copied from 2016 material. # 0.1 First code copied from 2016 material.
# #
@ -57,7 +58,7 @@ if (! require(httr, quietly=TRUE)) {
UniProtID <- "P39678" UniProtID <- "P39678"
URL <- "http://prosite.expasy.org/cgi-bin/prosite/PSScan.cgi" URL <- "https://prosite.expasy.org/cgi-bin/prosite/PSScan.cgi"
response <- POST(URL, response <- POST(URL,
body = list(meta = "opt1", body = list(meta = "opt1",
@ -148,7 +149,7 @@ features
# = 2 Task solutions ====================================================== # = 2 Task solutions ======================================================
# I have placed such a function into the dbUtilities script: look it up by # I have placed such a function into the ABC-dbUtilities.R script: look it up by
# clicking on dbFetchPrositeFeatures() in the Environment pane. # clicking on dbFetchPrositeFeatures() in the Environment pane.
# Test: # Test:

2
scripts/ABC-dbUtilities.R
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@ -251,7 +251,7 @@ dbFetchPrositeFeatures <- function(ID) {
# psName char PROSITE motif name # psName char PROSITE motif name
# If the operation is not successful, a 0-length data frame is returned. # If the operation is not successful, a 0-length data frame is returned.
URL <- "http://prosite.expasy.org/cgi-bin/prosite/PSScan.cgi" URL <- "https://prosite.expasy.org/cgi-bin/prosite/PSScan.cgi"
response <- POST(URL, response <- POST(URL,
body = list(meta = "opt1", body = list(meta = "opt1",