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Maintainance fixes and UniProt API change bugfix

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This commit is contained in:
hyginn 2018-10-30 21:27:42 -04:00
parent ead20d5f18
commit 1dd87e7473
8 changed files with 51 additions and 30 deletions
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2
.utilities.R
View File

@ -93,7 +93,7 @@ pBar <- function(i, l, nCh = 50) {
ticks <- round(seq(1, l-1, length.out = nCh))
if (i < l) {
if (any(i == ticks)) {
p <- which(i == ticks)
p <- which(i == ticks)[1] # use only first, in case there are ties
p1 <- paste(rep("#", p), collapse = "")
p2 <- paste(rep("-", nCh - p), collapse = "")
cat(sprintf("\r|%s%s|", p1, p2))

37
BIN-Data_integration.R
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@ -3,12 +3,13 @@
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-Data_integration unit.
#
# Version: 1.0
# Version: 1.0.1
#
# Date: 2017 10 08
# Date: 2018 10 30
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 1.0.1 Bugfix: UniProt ID Mapping service API change
# 1.0 First live version
#
#
@ -28,10 +29,10 @@
#TOC> ==========================================================================
#TOC>
#TOC> Section Title Line
#TOC> -------------------------------------------
#TOC> 1 Identifier mapping 45
#TOC> 2 Cross-referencing tables 151
#TOC> Section Title Line
#TOC> -------------------------------------------------
#TOC> 1 Identifier mapping 40
#TOC> 2 Cross-referencing tables 164
#TOC>
#TOC> ==========================================================================
@ -73,14 +74,14 @@ myQueryIDs <- "NP_010227 NP_00000 NP_011036"
# the URL of the server and send a list of items labelled as "query" in the body
# of the request. GET() and POST() are functions from httr.
URL <- "http://www.uniprot.org/mapping/"
URL <- "https://www.uniprot.org/mapping/"
response <- POST(URL,
body = list(from = "P_REFSEQ_AC", # Refseq Protein
to = "ACC", # UniProt ID
format = "tab",
query = myQueryIDs))
response
cat(content(response))
# We need to check the status code - if it is not 200, an error ocurred and we
# can't process the result:
@ -94,6 +95,22 @@ myMappedIDs <- read.delim(file = textConnection(content(response)),
stringsAsFactors = FALSE)
myMappedIDs
# We actually only need columns 1 and 3, and we can also change the names
# to "From" and "To":
myMappedIDs <- myMappedIDs[ , c(1,3)]
colnames(myMappedIDs) <- c("From", "To")
myMappedIDs
# If this works as expected, you should see:
# From To
# 1 NP_010227 P39678
# 2 NP_011036 P25302
#
# ... and note that there are only two entries, because nothing was returned
# for the dummy "RefSeq ID" NP_00000
# If the query can't be fulfilled because of a problem with the server, a
# WebPage is returned. But the server status is also returned and we can check
# the status code. I have lately gotten many "503" status codes: Server Not
@ -114,7 +131,7 @@ myIDmap <- function (s, mapFrom = "P_REFSEQ_AC", mapTo = "ACC") {
# empty data frame if the mapping was unsuccessful. No rows are returned
# for IDs that are not mapped.
URL <- "http://www.uniprot.org/mapping/"
URL <- "https://www.uniprot.org/uploadlists/"
response <- POST(URL,
body = list(from = mapFrom,
to = mapTo,
@ -125,6 +142,8 @@ myIDmap <- function (s, mapFrom = "P_REFSEQ_AC", mapTo = "ACC") {
myMap <- read.delim(file = textConnection(content(response)),
sep = "\t",
stringsAsFactors = FALSE)
myMap <- myMap[ , c(1,3)]
colnames(myMap) <- c("From", "To")
} else {
myMap <- data.frame()
warning(paste("No uniProt ID mapping returned:",

4
FND-STA-Probability_distribution.R
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@ -584,8 +584,8 @@ KLdiv(pmfL1, pmfL2) # 0.1087
# random samples according to the rL1 distribution, calculate the Kullback
# Leibler divergence with countsL1, and compare the distribution we get with the
# value we observed as the difference with discL2. Essentially, this tells us
# the probability that countsL2 is actually a sample from the L1 function. Here we
# go:
# the probability that countsL2 is actually a sample from the L1 function.
# Here we go:
N <- 1000
divs <- numeric(N)

6
RPR-Biostrings.R
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@ -26,7 +26,7 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> ---------------------------------------------------------
#TOC> 1 The Biostrings Package 52
@ -41,7 +41,7 @@
#TOC> 5.1 Views 183
#TOC> 5.2 Iranges 195
#TOC> 5.3 StringSets 201
#TOC>
#TOC>
#TOC> ==========================================================================
@ -182,7 +182,7 @@ toString(myDNAseq[4:15])
# == 5.1 Views =============================================================
# Biostring "Views" are objects that store mutliple substrings of one
# Biostring "Views" are objects that store multiple substrings of one
# Biostring object.
(myView <- Views(myDNAseq, start = c(1, 19, 37), end = c(15, 30, 45)))

17
RPR-FASTA.R
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@ -12,7 +12,8 @@
# 1.0 New unit.
#
#
# TODO:
# TODO: Make a simple solution first, then extend it to error checking, and
# to handle .mfa files.
#
#
# == DO NOT SIMPLY source() THIS FILE! =======================================
@ -22,17 +23,17 @@
# going on. That's not how it works ...
#
# ==============================================================================
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> -------------------------------------
#TOC> 1 Reading FASTA 39
#TOC> 2 Interpreting FASTA 227
#TOC> 3 Writing FASTA 248
#TOC>
#TOC>
#TOC> ==========================================================================
@ -231,7 +232,7 @@ refAPSES[grep("P39678", refAPSES) + 1] # grep() the string and add 1
# when working with strings, we can use substr(<string>, <start>, <stop>) to
# extract substrings, but more often we expand the string into a vector of
# single characters with strsplit(<string>, ""). strsplit() returns a list,
# to accommodate that <string> could be a vector of many elements, therafore
# to accommodate that <string> could be a vector of many elements, therefore
# we usually unlist() the result if we use it only on a single string.
# Example: How many positive charged residues in "MBP1_SACCE"?
@ -297,8 +298,8 @@ writeFASTA <- function(s, OUT = stdout(), width = 60) {
}
# Let's try this. We don't define OUT, so the result is written to the console
# by default. Defualt width for sequence is 60 characters
# Let's try this. If we don't specify OUT, the result is written to the console
# by default. Default width for sequence is 60 characters
writeFASTA(refAPSES)

4
RPR-RegEx.R
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@ -63,8 +63,8 @@ IHKYRRIIREGTEMNIEEVDSSLDVILQTLIANNNKNKGAEQIITISNANSHA"
nchar(s)
# Must be 969
# Fetch the Uniprot ID by retrieving the first string that appears between two
# vertical bars in the header line.
# Task: Fetch the Uniprot ID by retrieving the first string that appears between
# two vertical bars ("pipes") in the header record.
#
# Develop the regular expression:

7
RPR-Unit_testing.R
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@ -25,13 +25,13 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> -------------------------------------------
#TOC> 1 Unit Tests with testthat 43
#TOC> 2 Organizing your tests 156
#TOC> 3 Task solutions 181
#TOC>
#TOC>
#TOC> ==========================================================================
@ -107,8 +107,7 @@ expect_error(log(v[1,2])) # This appears oK, but ...
expect_error(log(v[1,2]), "non-numeric") # ... it's actually a different error!
# Producing unit tests simply means: we define a function, and then we check
# whether all test pass. Consider a function that is loaded from your utilities
# file:
# whether all test pass. Consider a function that is loaded on startup:
biCode

4
scripts/ABC-dbUtilities.R
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@ -345,7 +345,7 @@ UniProtIDmap <- function (s, mapFrom = "P_REFSEQ_AC", mapTo = "ACC") {
# empty data frame if the mapping was unsuccessful. No rows are returned
# for IDs that are not mapped.
URL <- "http://www.uniprot.org/mapping/"
URL <- "https://www.uniprot.org/uploadlists/"
response <- POST(URL,
body = list(from = mapFrom,
to = mapTo,
@ -356,6 +356,8 @@ UniProtIDmap <- function (s, mapFrom = "P_REFSEQ_AC", mapTo = "ACC") {
myMap <- read.delim(file = textConnection(content(response)),
sep = "\t",
stringsAsFactors = FALSE)
myMap <- myMap[ , c(1,3)]
colnames(myMap) <- c("From", "To")
} else {
myMap <- data.frame()
warning(paste("No uniProt ID mapping returned:",