Fixed parsing and added missing logic
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hyginn
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@ -3,12 +3,13 @@
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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: 1.0
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# Version: 1.1
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#
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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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# 1.1 Fixed parsing logic.
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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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@ -26,14 +27,14 @@
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#TOC> ==========================================================================
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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 Preparations 41
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#TOC> 2 Defining the APSES domain 54
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#TOC> 3 Executing the BLAST search 76
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#TOC> 4 Analysing results 98
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#TOC>
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#TOC>
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#TOC> ==========================================================================
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@ -83,23 +84,20 @@ source("./scripts/BLAST.R")
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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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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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BLASTresults <- 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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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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length(BLASTresults$hits) # There should be at least one hit there. Ask for advice
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# in case this step fails.
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# = 4 Analysing results ===================================================
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# The BLAST.R script has defined a convenience function to parse BLAST
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# alignments.
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(topHit <- parseBLASTalignment(BLASThits, idx = 1)) # Parse the top hit
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(topHit <- BLASTresults$hits[[1]]) # Get 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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@ -7,11 +7,12 @@
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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: 2.1
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# Date: 2016 09 - 2017 10
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# Version: 3
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# Date: 2016 09 - 2017 11
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# Author: Boris Steipe
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#
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# Versions:
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# 3 parsing logic had not been fully implemented; Fixed.
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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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@ -44,9 +45,6 @@ BLAST <- function(q,
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myTimeout = 120) {
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# Purpose:
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# Basic BLAST search
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# Version: 2.0
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# Date: 2017-09
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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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@ -258,11 +256,10 @@ BLAST <- function(q,
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return(results)
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}
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parseBLASTalignment <- function(hits, idx) {
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# Parse one BLAST hit from a BLAST result
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parseBLASTalignment <- function(hit) {
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# Parse data from a character vector containing a BLAST hit
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# Parameters:
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# hits list contains the BLAST hits
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# idx int index of the requested hit
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# hit char one BLAST hit as char vector
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# Value:
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# list $def chr defline
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# $accession chr accession number
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@ -278,12 +275,20 @@ parseBLASTalignment <- function(hits, idx) {
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# $midSeq chr midline string
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# $Sseq chr subject sequence
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getToken <- function(patt, v) {
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# get the first token identified by pattern patt in character vector v
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v <- v[grep(patt, v)]
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if (length(v) > 1) { v <- v[1] }
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if (length(v) == 0) { token <- NA
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} else {
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token <- regmatches(v, regexec(patt, v))[[1]][2] }
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return(token)
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}
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h <- list()
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hit <- hits$hits[[idx]]
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# FASTA defline
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h$def <- hit$def
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h$def <- hit[1]
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# accesion number (ID), use the first if there are several, separated by "|"
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patt <- "^>(.+?)(\\s|\\|)" # from ">" to space or "|"
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@ -304,24 +309,46 @@ parseBLASTalignment <- function(hits, idx) {
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}
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# E-value
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h$E <- hit$E
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h$E <- as.numeric(getToken("Expect\\s*=(.+?), Method", hit))
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# length of hit and # identities
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h$lengthAli <- hit$lengthAli
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h$nIdentities <- hit$nIdentities
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# length of alignment
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h$lengthAli <- as.numeric(getToken("^\\s*Length\\s*=(.+)$", hit))
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# number of identities
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h$nIdentities <- as.numeric(getToken("^\\s*Identities\\s*=(.+?)/", hit))
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# number of gaps
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h$nGaps <- hit$nGaps
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h$nGaps <- as.numeric(getToken("\\s*Gaps\\s*=(.+?)/", hit))
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# split up alignment section
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idx <- grep("^Query ", hit)
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Que <- hit[idx]
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Mid <- hit[idx + 1]
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Sbj <- hit[idx + 2]
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# first and last positions
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h$Qbounds <- hit$Qbounds
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h$Sbounds <- hit$Sbounds
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h$Qbounds <- c(start = 0, end = 0)
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h$Qbounds[1] <- as.numeric(getToken("^Query\\s*(\\d+)", Que[1]))
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h$Qbounds[2] <- as.numeric(getToken("\\s*(\\d+)\\s*$", Que[length(Que)]))
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h$Sbounds <- c(start = 0, end = 0)
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h$Sbounds[1] <- as.numeric(getToken("^Sbjct\\s*(\\d+)", Sbj[1]))
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h$Sbounds[2] <- as.numeric(getToken("\\s*(\\d+)\\s*$", Sbj[length(Sbj)]))
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# aligned sequences
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for (i in seq_along(Que)) {
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patt <- ("^\\s*Query\\s*\\d+\\s*([A-Za-z-]+)") # capture aligned string
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m <- regexec(patt, Que[i])
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iFirst <- m[[1]][2]
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iLast <- iFirst + attr(m[[1]], which = "match.length")[2] - 1
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Que[i] <- substring(Que[i], iFirst, iLast)
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Mid[i] <- substring(Mid[i], iFirst, iLast)
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Sbj[i] <- substring(Sbj[i], iFirst, iLast)
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}
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h$Qseq <- hit$Qseq
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h$midSeq <- hit$midSeq
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h$Sseq <- hit$Sseq
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h$Qseq <- paste0(Que, collapse = "")
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h$midSeq <- paste0(Mid, collapse = "")
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h$Sseq <- paste0(Sbj, collapse = "")
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return(h)
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}
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