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hyginn 2019-11-14 22:40:45 -05:00
parent bae2d33f14
commit 5b197b8829
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BIN-ALI-Optimal_sequence_alignment.R
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@ -3,12 +3,13 @@
# Purpose: A Bioinformatics Course: # Purpose: A Bioinformatics Course:
# R code accompanying the BIN-ALI-Optimal_sequence_alignment unit. # 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) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 1.6 Maintenance
# 1.5 Change from require() to requireNamespace(), # 1.5 Change from require() to requireNamespace(),
# use <package>::<function>() idiom throughout # use <package>::<function>() idiom throughout
# 1.4 Pull s2c() from seqinr package, rather then loading the # 1.4 Pull s2c() from seqinr package, rather then loading the
@ -37,16 +38,16 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> -------------------------------------------------------------------------- #TOC> --------------------------------------------------------------------------
#TOC> 1 Prepare 54 #TOC> 1 Prepare 55
#TOC> 2 Biostrings Pairwise Alignment 71 #TOC> 2 Biostrings Pairwise Alignment 72
#TOC> 2.1 Optimal global alignment 89 #TOC> 2.1 Optimal global alignment 90
#TOC> 2.2 Optimal local alignment 152 #TOC> 2.2 Optimal local alignment 153
#TOC> 3 APSES Domain annotation by alignment 176 #TOC> 3 APSES Domain annotation by alignment 177
#TOC> 4 Update your database script 257 #TOC> 4 Update your database script 258
#TOC> 4.1 Preparing an annotation file ... 263 #TOC> 4.1 Preparing an annotation file ... 264
#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 265 #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 308 #TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 309
#TOC> 4.2 Execute and Validate 332 #TOC> 4.2 Execute and Validate 333
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -125,17 +126,17 @@ ali1@pattern@mismatch
# or work with "normal" R functions # or work with "normal" R functions
# the alignment length # the alignment length
nchar(ali1@pattern) nchar(as.character(ali1@pattern))
# the number of identities # the number of identities
sum(s2c(as.character(ali1@pattern)) == sum(seqinr::s2c(as.character(ali1@pattern)) ==
s2c(as.character(ali1@subject))) seqinr::s2c(as.character(ali1@subject)))
# ... e.g. to calculate the percentage of identities # ... e.g. to calculate the percentage of identities
100 * 100 *
sum(s2c(as.character(ali1@pattern)) == sum(seqinr::s2c(as.character(ali1@pattern)) ==
s2c(as.character(ali1@subject))) / seqinr::s2c(as.character(ali1@subject))) /
nchar(ali1@pattern) nchar(as.character(ali1@pattern))
# ... which should be the same as reported in the writePairwiseAlignments() # ... which should be the same as reported in the writePairwiseAlignments()
# output. Awkward to type? Then it calls for a function: # output. Awkward to type? Then it calls for a function:
# #
@ -144,7 +145,7 @@ percentID <- function(al) {
return(100 * return(100 *
sum(seqinr::s2c(as.character(al@pattern)) == sum(seqinr::s2c(as.character(al@pattern)) ==
seqinr::s2c(as.character(al@subject))) / seqinr::s2c(as.character(al@subject))) /
nchar(al@pattern)) nchar(as.character(al@pattern)))
} }
percentID(ali1) percentID(ali1)