From 40b9e6fc04efc647c25c7d83ab995be76b3a1155 Mon Sep 17 00:00:00 2001 From: hyginn Date: Thu, 16 Nov 2017 16:37:53 -0500 Subject: [PATCH] update to function <- package::function idiom --- BIN-ALI-Optimal_sequence_alignment.R | 49 +++++++++++++--------------- 1 file changed, 22 insertions(+), 27 deletions(-) diff --git a/BIN-ALI-Optimal_sequence_alignment.R b/BIN-ALI-Optimal_sequence_alignment.R index ce37582..ef9fb11 100644 --- a/BIN-ALI-Optimal_sequence_alignment.R +++ b/BIN-ALI-Optimal_sequence_alignment.R @@ -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 "-Annotations.json" in the