Updates for BIN-ALI-BLAST
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BIN-ALI-BLAST.R
273
BIN-ALI-BLAST.R
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# Purpose: A Bioinformatics Course:
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# R code accompanying the BIN-ALI-BLAST unit.
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#
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# Version: 0.1
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# Version: 1.0
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#
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# Date: 2017 08 28
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# Date: 2017 10 23
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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#
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# Versions:
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# 1.0 First live version 2017.
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# 0.1 First code copied from 2016 material.
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#
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#
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# TODO:
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#
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#
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# == DO NOT SIMPLY source() THIS FILE! =======================================
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#
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# If there are portions you don't understand, use R's help system, Google for an
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# answer, or ask your instructor. Don't continue if you don't understand what's
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# going on. That's not how it works ...
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# ==============================================================================
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# = 1 ___Section___
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# BLAST.R
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#
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# Purpose: Send off one BLAST search and return parsed list of results
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# This script uses the BLAST URL-API
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# (Application Programming Interface) at the NCBI.
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# Read about the constraints here:
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# http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYP=DeveloperInfo
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#
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#
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# Version: 1.0
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# Date: 2016-09
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# Author: Boris Steipe
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#
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#
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# ToDo:
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# Notes: The bioconducter "annotate" package contains code for BLAST searches,
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# in case you need to do something more involved.
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#
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# ==============================================================================
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#TOC> ==========================================================================
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#TOC>
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#TOC> Section Title Line
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#TOC> ---------------------------------------------
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#TOC> 1 Packages 41
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#TOC> 2 Defining the APSES domain 50
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#TOC> 3 Executing the BLAST search 72
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#TOC> 4 Analysing results 94
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#TOC>
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#TOC> ==========================================================================
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# Dependencies: myEmail must exist as a global variable with
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# your valid email adress
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# waitTimer() must be loaded (it should have been loaded from
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# .utilities.R, which was sourced via .Rprofile)
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# = 1 Packages ============================================================
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# library to interface with WebServers and process their XML/HTML
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# responses
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if (!require(xml2, quietly = TRUE)) {
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install.packages("xml2")
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library(xml2)
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}
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if (!require(httr, quietly = TRUE)) {
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install.packages("httr")
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library(httr)
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if (!require(Biostrings, quietly=TRUE)) {
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source("https://bioconductor.org/biocLite.R")
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biocLite("Biostrings")
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library(Biostrings)
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}
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# = 2 Defining the APSES domain ===========================================
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parseBLAST_XML <- function(hit) {
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# parse one BLAST hit XML node with the xml2 package;
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# return a list
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# Load your protein database
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source("makeProteinDB.R")
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h <- list()
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h$id <- xml_text(xml_find_first(hit, ".//Hit_accession"))
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h$def <- xml_text(xml_find_first(hit, ".//Hit_def"))
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h$bestE <- Inf
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h$sumLen <- 0
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h$sumId <- 0
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h$sumGap <- 0
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hsps <- xml_find_all(hit, ".//Hsp")
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h$Hsp <- list()
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h$nHsps <- length(hsps)
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if (h$nHsps > 0) {
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for (i in 1:length(hsps)) {
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h$Hsp[[i]] <- list()
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h$Hsp[[i]]$e <- xml_numeric(hsps[i], ".//Hsp_evalue")
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h$Hsp[[i]]$q_from <- xml_numeric(hsps[i], ".//Hsp_query-from")
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h$Hsp[[i]]$q_to <- xml_numeric(hsps[i], ".//Hsp_query-to")
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h$Hsp[[i]]$h_from <- xml_numeric(hsps[i], ".//Hsp_hit-from")
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h$Hsp[[i]]$h_to <- xml_numeric(hsps[i], ".//Hsp_hit-to")
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h$Hsp[[i]]$h_identity <- xml_numeric(hsps[i], ".//Hsp_identity")
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h$Hsp[[i]]$h_gaps <- xml_numeric(hsps[i], ".//Hsp_gaps")
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h$Hsp[[i]]$h_len <- xml_numeric(hsps[i], ".//Hsp_align-len")
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h$Hsp[[i]]$qseq <- xml_text(xml_find_first(hsps[i], ".//Hsp_qseq"))
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h$Hsp[[i]]$mid <- xml_text(xml_find_first(hsps[i], ".//Hsp_midline"))
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h$Hsp[[i]]$hseq <- xml_text(xml_find_first(hsps[i], ".//Hsp_hseq"))
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# Get the APSES domain sequence for MBP1_MYSPE feature annotation. (You have
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# entered this data in the BIN-ALI-Optimal_sequence_alignment unit.)
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h$bestE <- min(h$bestE, h$Hsp[[i]]$e)
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h$sumLen <- h$sumLen + h$Hsp[[i]]$h_len
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h$sumId <- h$sumId + h$Hsp[[i]]$h_identity
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h$sumGap <- h$sumGap + h$Hsp[[i]]$h_gaps
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}
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}
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return(h)
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}
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(proID <- myDB$protein$ID[myDB$protein$name == "MBP1_<MYSSPE>"]) # <<< EDIT
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(ftrID <- myDB$feature$ID[myDB$feature$name == "APSES fold"])
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(fanID <- myDB$annotation$ID[myDB$annotation$proteinID == proID &
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myDB$annotation$featureID == ftrID])
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(start <- myDB$annotation$start[myDB$annotation$ID == fanID])
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(end <- myDB$annotation$end[myDB$annotation$ID == fanID])
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(apses <- substr(myDB$protein$sequence[myDB$protein$ID == proID],
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start,
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end))
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xml_numeric <- function(n, p) {
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# Utility: return first node matching xpath p in XML node n as numeric
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return(as.numeric(xml_text(xml_find_first(n, p))))
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}
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# The MYSPE "apses" sequence is the sequence that we will use for our reverse
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# BLAST search.
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BLAST <- function(q,
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db = "refseq_protein",
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nHits = 30,
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E = 3,
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limits = "\"\"",
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email = myEMail,
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rid = "",
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quietly = FALSE) {
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# Purpose:
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# Basic BLAST search
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# Version: 1.0
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# Date: 2016-09
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# Author: Boris Steipe
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#
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# Parameters:
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# q: query - either a valid ID or a sequence
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# db: "refseq_protein" by default,
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# other legal valuses include: "nr", "pdb", "swissprot" ...
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# nHits: number of hits to maximally return
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# E: E-value cutoff. Do not return hits whose score would be expected
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# to occur E or more times in a database of random sequence.
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# limits: a valid ENTREZ filter
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# email: a valid email address, defaults to global value myEMail
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# quietly: controls printing of wait-time progress bar
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# Value:
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# result: list of resulting hits and some metadata
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# = 3 Executing the BLAST search ==========================================
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results <- list()
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results$rid <- rid
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results$rtoe <- 0
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# The ./scripts/BLAST.R code defines two functions to access the BLAST interface
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# through its Web API, and to parse results. Have a look at the script, then
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# source it:
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if (rid == "") { # prepare, send and analyse query
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results$query <- paste(
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"https://www.ncbi.nlm.nih.gov/blast/Blast.cgi",
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"?",
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"QUERY=", q,
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"&DATABASE=", db,
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"&HITLIST_SIZE=", as.character(nHits),
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"&EXPECT=", as.character(E),
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"&PROGRAM=", "blastp",
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"&ENTREZ_QUERY=", limits,
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"&NOHEADER=", "true",
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"&EMAIL=", email,
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"&CMD=Put",
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sep = "")
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source("./scripts/BLAST.R")
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# send it off ...
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response <- read_xml(results$query, as_html = TRUE)
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# Use BLAST() to find the best match to the MYSPE APSES domain in Saccharomyces
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# cerevisiae:
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# find the comment node that contains the information we need
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# using an xpath expression
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info <- xml_find_first(response,
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"//comment()[contains(., \"QBlastInfo\")]")
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info <- xml_text(info) # extract its contents
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# parse
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results$rid <- regmatches(info,
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regexec("RID = (\\w+)", info))[[1]][2]
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results$rtoe <- regmatches(info,
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regexec("RTOE = (\\d+)", info))[[1]][2]
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results$rtoe <- as.numeric(results$rtoe)
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} # done analysing query
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# Now we wait ...
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if (quietly) {
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Sys.sleep(results$rtoe)
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} else {
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cat(sprintf("BLAST is processing %s:\n", results$rid))
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waitTimer(results$rtoe)
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}
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# retrieve results from BLAST server
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URL <- paste("https://www.ncbi.nlm.nih.gov/blast/Blast.cgi",
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"?",
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"RID=", results$rid,
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"&FORMAT_TYPE=", "XML",
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"&EMAIL=", email,
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"&CMD=Get",
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sep = "")
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raw <- GET(URL)
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timeOut <- 300
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nWait <- 0
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while (raw$headers["content-type"] == "text/html" && nWait <= (timeOut/10)) {
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cat("Doesn't seem to be done. Wait some more (or click STOP to abort)\n")
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waitTimer(10)
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nWait <- nWait + 1
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raw <- GET(URL)
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}
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# If we get to here, we received some result. But what?
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if (raw$headers["content-type"] == "text/html") { # Still HTML? Didn't complete ...
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stop(sprintf("Query >>%s<< didn't complete.", results$rid))
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} else if (raw$headers["content-type"] == "application/xml") { # Good!
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response <- read_xml(raw)
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} else { # Unknown, abort.
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stop(sprintf("Unknown response type: >>%s<<.", raw$headers["content-type"]))
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}
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hits <- xml_find_all(response, ".//Hit")
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if (length(hits) == 0) {
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s <- "No hit returned.\n"
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s <- c(s, sprintf("Check your query string:\n>>%s<<\n", results$query))
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s <- c(s, sprintf("and/or try again later by typing:\n", results$rid))
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s <- c(s, sprintf(" BLAST(rid = \"%s\")\n", results$rid))
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stop(paste(s, collapse = ""))
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}
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results$hits <- list()
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for (i in 1:length(hits)) {
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results$hits[[i]] <- parseBLAST_XML(hits[i])
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}
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return(results)
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}
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BLASThits <- BLAST(apses, # MYSPE APSES domain sequence
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db = "refseq_protein", # database to search in
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nHits = 10, #
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E = 0.01, #
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limits = "txid559292[ORGN]") # S. cerevisiae S288c
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# = 1 Tasks
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length(BLASThits) # There should be at least one hit there. Ask for advice
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# in case this step fails.
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# = 4 Analysing results ===================================================
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# The BLAST.R script has defined a convenience function to parse BLAST
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# alignments.
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(topHit <- parseBLASTalignment(BLASThits, idx = 1)) # Parse the top hit
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# What is the refseq ID of the top hit
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topHit$accession
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# If this is "NP_010227.1" you have confirmed the RBM of the MYSPE apses
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# domain. If it is not, ask me for advice.
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# ==== TESTS ===================================================================
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# q <- paste("IYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHI", # Mbp1 APSES domain
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# "LKAANFAKAKRTRILEKEVLKETHEKVQGGFGKYQ",
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# "GTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASP",
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# sep="")
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# q <- "NP_010227"
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# fungi <- "txid4751[ORGN]"
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#
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# test <- BLAST("NP_010227",
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# nHits = 1000,
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# E = 0.01,
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# limits = fungi)
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# length(test$hits)
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17
BIN-MYSPE.R
17
BIN-MYSPE.R
@ -3,12 +3,13 @@
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# Purpose: A Bioinformatics Course:
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# R code accompanying the BIN-MYSPE unit
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#
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# Version: 1.0
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# Version: 1.0.1
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#
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# Date: 2017 09 21
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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#
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# V 1.0 Final code, after rewriting BLAST parser and creating current MYSPElist
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# V 1.0.1 Move ABC-makeMYSPElist.R to ./scripts directory
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# V 1.0 Final code, after rewriting BLAST parser and updating MYSPElist
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# V 0.1 First code copied from BCH441_A03_makeMYSPElist.R
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#
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# TODO:
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@ -28,9 +29,9 @@
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#TOC>
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#TOC> Section Title Line
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#TOC> ---------------------------------------
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#TOC> 1 Preparations 38
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#TOC> 2 Suitable MYSPE Species 50
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#TOC> 3 Adopt "MYSPE" 64
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#TOC> 1 Preparations 39
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#TOC> 2 Suitable MYSPE Species 51
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#TOC> 3 Adopt "MYSPE" 65
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#TOC>
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#TOC> ==========================================================================
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@ -56,10 +57,10 @@ if (! exists("myStudentNumber")) {
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# A detailed description of the process of compiling the list of genome
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# sequenced fungi with protein annotations and Mbp1 homologues is in the file
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# ABC-makeMYSPElist.R
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# ./scripts/ABC-makeMYSPElist.R
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# Task: Study ABC-makeMYSPElist.R, it implements a rather typical workflow of
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# selecting and combining data from various public-domain data resources.
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# Task: Study ./scripts/ABC-makeMYSPElist.R, it implements a typical workflow
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# of selecting and combining data from public-domain data resources.
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# = 3 Adopt "MYSPE" =======================================================
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@ -71,8 +71,8 @@
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{"pName" : "MBP1_COPCI", "fName" : "coiled coil", "start" : "500", "end" : "570"},
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{"pName" : "MBP1_COPCI", "fName" : "coiled coil", "start" : "651", "end" : "678"},
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{"pName" : "MBP1_CRYNE", "fName" : "APSES fold", "start" : "113", "end" : "211"},
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{"pName" : "MBP1_CRYNE", "fName" : "KilA-N", "start" : "131", "end" : "215"},
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{"pName" : "MBP1_CRYNE", "fName" : "APSES fold", "start" : "16", "end" : "114"},
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{"pName" : "MBP1_CRYNE", "fName" : "KilA-N", "start" : "34", "end" : "117"},
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{"pName" : "MBP1_CRYNE", "fName" : "low complexity", "start" : "66", "end" : "85"},
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{"pName" : "MBP1_CRYNE", "fName" : "low complexity", "start" : "413", "end" : "423"},
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{"pName" : "MBP1_CRYNE", "fName" : "low complexity", "start" : "633", "end" : "644"},
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# Purpose: Create a list of genome sequenced fungi with protein annotations and
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# Mbp1 homologues.
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#
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# Version: 1.1.1
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# Version: 1.1.2
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#
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# Date: 2016 09 - 2017 09
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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#
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# V 1.1.2 Moved BLAST.R to ./scripts directory
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# V 1.1 Update 2017
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# V 1.0 First code 2016
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#
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@ -184,12 +185,12 @@ length(GOLDspecies)
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# amount of error handling involved that is not supported by the API in a
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# principled way but requires rather ad hoc solutions. The code I threw together
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# to make a BLAST interface (demo-quality, not research-quality) is in the file
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# BLAST.R Feel encouraged to study how this works. It's a pretty standard task
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# of communicating with servers and parsing responses - everyday fare in the
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# bioinformatics lab. Surprisingly, there seems to be no good BLAST parser
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# in currently available packages.
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# ./scripts/BLAST.R Feel encouraged to study how this works. It's a pretty
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# standard task of communicating with servers and parsing responses - everyday
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# fare in thebioinformatics lab. Surprisingly, there seems to be no good BLAST
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# parser in currently available packages.
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# source("BLAST.R") # load the function and its utilities
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# source("./scripts/BLAST.R") # load the function and its utilities
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# Use BLAST() to find yeast Mbp1 homologues in other fungi in refseq
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# BLASThits <- BLAST("NP_010227", # Yeast Mbp1 RefSeq ID
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# db = "refseq_protein", # database to search in
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@ -4,14 +4,16 @@
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# This script uses the BLAST URL-API
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# (Application Programming Interface) at the NCBI.
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# Read about the constraints here:
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# https://ncbi.github.io/blast-cloud/dev/api.html
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# https://ncbi.github.io/blast-cloud/dev/api.html
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#
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#
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# Version: 2.0
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# Date: 2016 09 - 2017 09
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# Version: 2.1
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# Date: 2016 09 - 2017 10
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# Author: Boris Steipe
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#
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# Versions:
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# 2.1 bugfix in BLAST(), bug was blanking non-split deflines;
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# refactored parseBLASTalignment() to handle lists with multiple hits.
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# 2.0 Completely rewritten because the interface completely changed.
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# Code adpated in part from NCBI Perl sample code:
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# $Id: web_blast.pl,v 1.10 2016/07/13 14:32:50 merezhuk Exp $
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@ -68,8 +70,9 @@ BLAST <- function(q,
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results$rid <- rid
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results$rtoe <- 0
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if (rid == "") { # we skip, and proceed directly to retrieval
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# if rid is not the empty string
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if (rid == "") { # if rid is not the empty string we skip the
|
||||
# initial search and and proceed directly to retrieval
|
||||
|
||||
|
||||
# prepare query, GET(), and parse rid and rtoe from BLAST server response
|
||||
results$query <- paste0("https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi",
|
||||
@ -216,8 +219,10 @@ BLAST <- function(q,
|
||||
# Merge these lines to the preceding lines and delete them.
|
||||
#
|
||||
x <- which(grepl("]$", txt) & !(grepl("^>", txt)))
|
||||
txt[x-1] <- paste0(txt[x-1], txt[x])
|
||||
txt <- txt[-x]
|
||||
if (length(x) > 0) {
|
||||
txt[x-1] <- paste0(txt[x-1], txt[x])
|
||||
txt <- txt[-x]
|
||||
}
|
||||
|
||||
# Special case: there may be multiple deflines when the BLAST hit is to
|
||||
# redundant, identical sequences. Keep only the first instance.
|
||||
@ -253,18 +258,32 @@ BLAST <- function(q,
|
||||
return(results)
|
||||
}
|
||||
|
||||
parseBLASTalignment <- function(hit) {
|
||||
# parse one BLAST hit;
|
||||
# return a list
|
||||
|
||||
if (length(grep("Length", hit)) > 1) {
|
||||
stop("Parsing function can't handle multiple HSPs (yet).")
|
||||
}
|
||||
parseBLASTalignment <- function(hits, idx) {
|
||||
# Parse one BLAST hit from a BLAST result
|
||||
# Parameters:
|
||||
# hits list contains the BLAST hits
|
||||
# idx int index of the requested hit
|
||||
# Value:
|
||||
# list $def chr defline
|
||||
# $accession chr accession number
|
||||
# $organism chr complete organism definition
|
||||
# $species chr binomial species
|
||||
# $E num E value
|
||||
# $lengthAli num length of the alignment
|
||||
# $nIdentitites num number of identities
|
||||
# $nGaps num number of gaps
|
||||
# $Qbounds num 2-element vector of query start-end
|
||||
# $Sbounds num 2-element vector of subject start-end
|
||||
# $Qseq chr query sequence
|
||||
# $midSeq chr midline string
|
||||
# $Sseq chr subject sequence
|
||||
|
||||
h <- list()
|
||||
|
||||
hit <- hits$hits[[idx]]
|
||||
|
||||
# FASTA defline
|
||||
h$def <- hit[1]
|
||||
h$def <- hit$def
|
||||
|
||||
# accesion number (ID), use the first if there are several, separated by "|"
|
||||
patt <- "^>(.+?)(\\s|\\|)" # from ">" to space or "|"
|
||||
@ -276,70 +295,38 @@ parseBLASTalignment <- function(hit) {
|
||||
|
||||
# species
|
||||
x <- unlist(strsplit(h$organism, "\\s+"))
|
||||
if (length(x) < 2) {
|
||||
h$species <- NA
|
||||
if (length(x) >= 2) {
|
||||
h$species <- paste(x[1], x[2])
|
||||
} else if (length(x) == 1) {
|
||||
h$species <- paste(x[1], "sp.")
|
||||
} else {
|
||||
h$species <- paste(x[1:2], collapse = " ")
|
||||
h$species <- NA
|
||||
}
|
||||
|
||||
# E-value
|
||||
x <- hit[grep("Expect\\s*=", hit)]
|
||||
patt <- "Expect\\s*=\\s*([0-9.eE\\-]+)" #
|
||||
h$E <- as.numeric(regmatches(x, regexec(patt, x))[[1]][2])
|
||||
h$E <- hit$E
|
||||
|
||||
# length of hit and # identities
|
||||
x <- hit[grep("Identities\\s*=", hit)]
|
||||
patt <- "Identities\\s*=\\s*([0-9]+)/([0-9]+)"
|
||||
m <- regexec(patt, x)
|
||||
h$lengthAli <- as.numeric(regmatches(x, m)[[1]][2])
|
||||
h$nIdentities <- as.numeric(regmatches(x, m)[[1]][3])
|
||||
h$lengthAli <- hit$lengthAli
|
||||
h$nIdentities <- hit$nIdentities
|
||||
|
||||
# number of gaps
|
||||
x <- hit[grep("Gaps\\s*=", hit)]
|
||||
patt <- "Gaps\\s*=\\s*([0-9]+)"
|
||||
h$nGaps <- as.numeric(regmatches(x, regexec(patt, x))[[1]][2])
|
||||
h$nGaps <- hit$nGaps
|
||||
|
||||
# first and last positions
|
||||
iAli <- grep("^Query\\s+", hit)
|
||||
h$Qbounds <- getAliBounds(hit[iAli])
|
||||
h$Sbounds <- getAliBounds(hit[iAli + 2])
|
||||
h$Qbounds <- hit$Qbounds
|
||||
h$Sbounds <- hit$Sbounds
|
||||
|
||||
# aligned sequences
|
||||
|
||||
h$Qseq <- character()
|
||||
h$midSeq <- character()
|
||||
h$Sseq <- character()
|
||||
|
||||
for (i in iAli) {
|
||||
patt <- "^Query\\s+[0-9]+\\s*"
|
||||
first <- attr(regexec(patt, hit[i])[[1]], "match.length") + 1
|
||||
|
||||
patt <- "\\s*[0-9]*\\s*$"
|
||||
last <- regexec(patt, hit[i])[[1]][1] - 1
|
||||
|
||||
h$Qseq <- paste0(h$Qseq, substr(hit[i], first, last))
|
||||
h$midSeq <- paste0(h$midSeq, substr(hit[i + 1], first, last))
|
||||
h$Sseq <- paste0(h$Sseq, substr(hit[i + 2], first, last))
|
||||
}
|
||||
h$Qseq <- hit$Qseq
|
||||
h$midSeq <- hit$midSeq
|
||||
h$Sseq <- hit$Sseq
|
||||
|
||||
return(h)
|
||||
}
|
||||
|
||||
|
||||
getAliBounds <- function(s) {
|
||||
# get first and last position from a vector of BLAST alignments s
|
||||
# value: numeric vector of first and last position
|
||||
patt <- "^(Query|Sbjct)\\s+([0-9]+)\\s"
|
||||
first <- as.numeric(regmatches(s[1], regexec(patt, s[1]))[[1]][3])
|
||||
|
||||
patt <- "\\s*([0-9]+)\\s*$"
|
||||
last <- as.numeric(regmatches(s[length(s)],
|
||||
regexec(patt, s[length(s)]))[[1]][2])
|
||||
return(c (first, last))
|
||||
}
|
||||
|
||||
|
||||
|
||||
# ==== TESTS ===================================================================
|
||||
|
||||
# define query:
|
||||
Loading…
Reference in New Issue
Block a user