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load seqinr

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hyginn 2017-11-16 14:46:15 -05:00
parent a58e35f060
commit 4bbf663eca
1 changed files with 32 additions and 17 deletions
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BIN-ALI-Optimal_sequence_alignment.R
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@ -3,12 +3,13 @@
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-ALI-Optimal_sequence_alignment unit.
#
# Version: 1.1
# Version: 1.2
#
# Date: 2017 09 - 2017 11
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 1.2 Added missing load of seqinr package
# 1.1 Update annotation file logic - it could already have been
# prepared in the BIN-FUNC-Annotation unit.
# 1.0.1 bugfix
@ -28,25 +29,38 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> --------------------------------------------------------------------
#TOC> 1 Prepare 48
#TOC> 2 Biostrings Pairwise Alignment 56
#TOC> 2.1 Optimal global alignment 73
#TOC> 2.2 Optimal local alignment 136
#TOC> 3 APSES Domain annotation by alignment 160
#TOC> 4 Update your database script 241
#TOC> 4.1 Preparing an annotation file ... 247
#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 249
#TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 292
#TOC> 4.2 Execute and Validate 316
#TOC>
#TOC> 1 Prepare 49
#TOC> 2 Biostrings Pairwise Alignment 70
#TOC> 2.1 Optimal global alignment 88
#TOC> 2.2 Optimal local alignment 151
#TOC> 3 APSES Domain annotation by alignment 175
#TOC> 4 Update your database script 256
#TOC> 4.1 Preparing an annotation file ... 262
#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 264
#TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 307
#TOC> 4.2 Execute and Validate 331
#TOC>
#TOC> ==========================================================================
# = 1 Prepare =============================================================
# To simplify code a bit, we will use seqinr's function s2c(x) to make
# character vectors from sequence strings below, rather than the lengthier
# base idiom unlist(strsplit(x, "").
if (!require(seqinr)) {
install.packages("seqinr")
library(seqinr)
}
# Package information:
# library(help = seqinr) # basic information
# browseVignettes("seqinr") # available vignettes
# data(package = "seqinr") # available datasets
# You need to recreate the protein database that you have constructed in the
# BIN-Storing_data unit.
@ -55,6 +69,7 @@ source("makeProteinDB.R")
# = 2 Biostrings Pairwise Alignment =======================================
if (!require(Biostrings, quietly=TRUE)) {
if (! exists("biocLite")) {
source("https://bioconductor.org/biocLite.R")
@ -113,12 +128,12 @@ nchar(ali1@pattern)
# the number of identities
sum(s2c(as.character(ali1@pattern)) ==
s2c(as.character(ali1@subject)))
s2c(as.character(ali1@subject)))
# ... e.g. to calculate the percentage of identities
100 *
sum(s2c(as.character(ali1@pattern)) ==
s2c(as.character(ali1@subject))) /
s2c(as.character(ali1@subject))) /
nchar(ali1@pattern)
# ... which should be the same as reported in the writePairwiseAlignments()
# output. Awkward to type? Then it calls for a function:
@ -127,7 +142,7 @@ percentID <- function(al) {
# returns the percent-identity of a Biostrings alignment object
return(100 *
sum(s2c(as.character(al@pattern)) ==
s2c(as.character(al@subject))) /
s2c(as.character(al@subject))) /
nchar(al@pattern))
}
@ -289,7 +304,7 @@ aliApses@subject@range@start + aliApses@subject@range@width - 1
# Then SKIP the next section.
#
#
# === 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit
# === 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit
#
#
# You DO already have a file called "<MYSPE>-Annotations.json" in the