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update to function <- package::function idiom

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hyginn 2017-11-16 16:37:53 -05:00
parent 62a1a76558
commit 40b9e6fc04
1 changed files with 22 additions and 27 deletions
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BIN-ALI-Optimal_sequence_alignment.R
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@ -3,12 +3,14 @@
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-ALI-Optimal_sequence_alignment unit.
#
# Version: 1.3
# Version: 1.4
#
# Date: 2017 09 - 2017 11
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 1.4 Pull s2c() from seqinr package, rather then loading the
# entire library.
# 1.3 Updated confirmation task with correct logic
# 1.2 Added missing load of seqinr package
# 1.1 Update annotation file logic - it could already have been
@ -30,36 +32,29 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> --------------------------------------------------------------------
#TOC> 1 Prepare 50
#TOC> 2 Biostrings Pairwise Alignment 71
#TOC> 2.1 Optimal global alignment 89
#TOC> 2.2 Optimal local alignment 152
#TOC> 3 APSES Domain annotation by alignment 176
#TOC> 4 Update your database script 257
#TOC> 4.1 Preparing an annotation file ... 263
#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 265
#TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 308
#TOC> 4.2 Execute and Validate 332
#TOC>
#TOC> 1 Prepare 52
#TOC> 2 Biostrings Pairwise Alignment 66
#TOC> 2.1 Optimal global alignment 84
#TOC> 2.2 Optimal local alignment 147
#TOC> 3 APSES Domain annotation by alignment 171
#TOC> 4 Update your database script 252
#TOC> 4.1 Preparing an annotation file ... 258
#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 260
#TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 303
#TOC> 4.2 Execute and Validate 327
#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
# To simplify code, we pull the function s2c(x) from the seqinr package,
# rather than using the lengthier idiom unlist(strsplit(x, "").
# This assumes that the seqinr package has been installed previously.
s2c <- seqinr::s2c
# You need to recreate the protein database that you have constructed in the
@ -142,8 +137,8 @@ sum(s2c(as.character(ali1@pattern)) ==
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))) /
sum(seqinr::s2c(as.character(al@pattern)) ==
seqinr::s2c(as.character(al@subject))) /
nchar(al@pattern))
}
@ -305,7 +300,7 @@ 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