diff --git a/BIN-PHYLO-Tree_building.R b/BIN-PHYLO-Tree_building.R index ec5b014..5f013b1 100644 --- a/BIN-PHYLO-Tree_building.R +++ b/BIN-PHYLO-Tree_building.R @@ -79,7 +79,7 @@ if (!require(Rphylip, quietly=TRUE)) { # PROMLPATH <- "/Applications/phylip-3.695/exe/proml.app/Contents/MacOS" # === 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 # that is named "exe", and right-click to inspect its properties. The path # should be listed among them. diff --git a/BIN-Storing_data.R b/BIN-Storing_data.R index f61da14..e0cf4cf 100644 --- a/BIN-Storing_data.R +++ b/BIN-Storing_data.R @@ -180,9 +180,9 @@ autoincrement <- function(table) { autoincrement(philDB$person) # Once that is clear, let's remove the Zhuangzi entry and recreate it correctly. -# Many ways to remove, here we use a logical expression to select matching record(s), -# apply the results to subset the data frame, and overwrite the existing table -# with the new one. +# Many ways to remove, here we use a logical expression to select matching +# record(s), apply the results to subset the data frame, and overwrite the +# existing table with the new one. sel <- !(philDB$person$name == "Zhuangzi") # select ... philDB$person <- philDB$person[sel, ] # ... and replace @@ -260,7 +260,7 @@ philDB$books$title sel <- numeric() # initialize the vector for (ID in pID) { sel <- which(philDB$works$personID == ID) # get all rows for which - # the condition is TRUE + # the condition is TRUE cat(sprintf("%s: ", philDB$person$name[ID])) # output the person cat(sprintf("\"%s\" ", philDB$books$title[sel])) # output the book cat("\n") diff --git a/RPR-PROSITE_POST.R b/RPR-PROSITE_POST.R index 612ffc8..09116d9 100644 --- a/RPR-PROSITE_POST.R +++ b/RPR-PROSITE_POST.R @@ -3,12 +3,13 @@ # Purpose: A Bioinformatics Course: # 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) # # Versions: +# 1.0.1 Updates for slightly changed interfaces # 1.0 First ABC units version # 0.1 First code copied from 2016 material. # @@ -26,13 +27,13 @@ #TOC> ========================================================================== -#TOC> +#TOC> #TOC> Section Title Line #TOC> --------------------------------------------------------------- #TOC> 1 Constructing a POST command from a Web query 44 #TOC> 1.1 Task - fetchPrositeFeatures() function 145 #TOC> 2 Task solutions 153 -#TOC> +#TOC> #TOC> ========================================================================== @@ -57,7 +58,7 @@ if (! require(httr, quietly=TRUE)) { 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, body = list(meta = "opt1", @@ -148,7 +149,7 @@ features # = 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. # Test: diff --git a/scripts/ABC-dbUtilities.R b/scripts/ABC-dbUtilities.R index 3911119..2a582a5 100644 --- a/scripts/ABC-dbUtilities.R +++ b/scripts/ABC-dbUtilities.R @@ -251,7 +251,7 @@ dbFetchPrositeFeatures <- function(ID) { # psName char PROSITE motif name # 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, body = list(meta = "opt1",