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hyginn 2019-11-14 22:40:45 -05:00
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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: 1.5
# Version: 1.6
#
# Date: 2017 09 - 2019 01
# Date: 2017 09 - 2019 11
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 1.6 Maintenance
# 1.5 Change from require() to requireNamespace(),
# use <package>::<function>() idiom throughout
# 1.4 Pull s2c() from seqinr package, rather then loading the
@ -34,20 +35,20 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#TOC> --------------------------------------------------------------------------
#TOC> 1 Prepare 54
#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 55
#TOC> 2 Biostrings Pairwise Alignment 72
#TOC> 2.1 Optimal global alignment 90
#TOC> 2.2 Optimal local alignment 153
#TOC> 3 APSES Domain annotation by alignment 177
#TOC> 4 Update your database script 258
#TOC> 4.1 Preparing an annotation file ... 264
#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 266
#TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 309
#TOC> 4.2 Execute and Validate 333
#TOC>
#TOC> ==========================================================================
@ -125,17 +126,17 @@ ali1@pattern@mismatch
# or work with "normal" R functions
# the alignment length
nchar(ali1@pattern)
nchar(as.character(ali1@pattern))
# the number of identities
sum(s2c(as.character(ali1@pattern)) ==
s2c(as.character(ali1@subject)))
sum(seqinr::s2c(as.character(ali1@pattern)) ==
seqinr::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))) /
nchar(ali1@pattern)
sum(seqinr::s2c(as.character(ali1@pattern)) ==
seqinr::s2c(as.character(ali1@subject))) /
nchar(as.character(ali1@pattern))
# ... which should be the same as reported in the writePairwiseAlignments()
# output. Awkward to type? Then it calls for a function:
#
@ -144,7 +145,7 @@ percentID <- function(al) {
return(100 *
sum(seqinr::s2c(as.character(al@pattern)) ==
seqinr::s2c(as.character(al@subject))) /
nchar(al@pattern))
nchar(as.character(al@pattern)))
}
percentID(ali1)
@ -305,7 +306,7 @@ 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