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Updated logic

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hyginn 2017-11-16 16:01:56 -05:00
parent 4bbf663eca
commit 62a1a76558
1 changed files with 18 additions and 19 deletions
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37
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: 1.2
# Version: 1.3
#
# Date: 2017 09 - 2017 11
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 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
# prepared in the BIN-FUNC-Annotation unit.
@ -29,20 +30,20 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#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 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> ==========================================================================
@ -304,7 +305,7 @@ 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
@ -342,14 +343,12 @@ aliApses@subject@range@start + aliApses@subject@range@width - 1
# The following commands should retrieve the correct start and end
# coordinates and sequence of the MBP1_MYSPE APSES domain:
sel <- myDB$protein$name == paste("MBP1_", biCode(MYSPE), sep = "")
aaMBP1_MYSPE <- AAString(myDB$protein$sequence[sel])
sel <- which(myDB$protein$name == paste("MBP1_", biCode(MYSPE), sep = ""))
(proID <- myDB$protein$ID[myDB$protein$name == "MBP1_<MYSSPE>"]) # <<< EDIT
(proID <- myDB$protein$ID[sel])
(ftrID <- myDB$feature$ID[myDB$feature$name == "APSES fold"])
(fanID <- myDB$annotation$ID[myDB$annotation$proteinID == proID &
myDB$annotation$featureID == ftrID])
myDB$annotation$featureID == ftrID])
(start <- myDB$annotation$start[myDB$annotation$ID == fanID])
(end <- myDB$annotation$end[myDB$annotation$ID == fanID])
(apses <- substr(myDB$protein$sequence[myDB$protein$ID == proID],