Updated logic
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# Purpose: A Bioinformatics Course:
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# Purpose: A Bioinformatics Course:
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# R code accompanying the BIN-ALI-Optimal_sequence_alignment unit.
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# R code accompanying the BIN-ALI-Optimal_sequence_alignment unit.
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#
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#
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# Version: 1.2
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# Version: 1.3
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#
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#
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# Date: 2017 09 - 2017 11
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# Date: 2017 09 - 2017 11
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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#
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#
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# Versions:
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# Versions:
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# 1.3 Updated confirmation task with correct logic
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# 1.2 Added missing load of seqinr package
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# 1.2 Added missing load of seqinr package
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# 1.1 Update annotation file logic - it could already have been
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# 1.1 Update annotation file logic - it could already have been
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# prepared in the BIN-FUNC-Annotation unit.
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# prepared in the BIN-FUNC-Annotation unit.
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@ -32,16 +33,16 @@
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#TOC>
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#TOC>
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#TOC> Section Title Line
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#TOC> Section Title Line
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#TOC> --------------------------------------------------------------------
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#TOC> --------------------------------------------------------------------
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#TOC> 1 Prepare 49
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#TOC> 1 Prepare 50
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#TOC> 2 Biostrings Pairwise Alignment 70
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#TOC> 2 Biostrings Pairwise Alignment 71
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#TOC> 2.1 Optimal global alignment 88
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#TOC> 2.1 Optimal global alignment 89
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#TOC> 2.2 Optimal local alignment 151
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#TOC> 2.2 Optimal local alignment 152
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#TOC> 3 APSES Domain annotation by alignment 175
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#TOC> 3 APSES Domain annotation by alignment 176
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#TOC> 4 Update your database script 256
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#TOC> 4 Update your database script 257
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#TOC> 4.1 Preparing an annotation file ... 262
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#TOC> 4.1 Preparing an annotation file ... 263
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#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 264
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#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 265
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#TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 307
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#TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 308
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#TOC> 4.2 Execute and Validate 331
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#TOC> 4.2 Execute and Validate 332
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#TOC>
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#TOC>
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#TOC> ==========================================================================
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#TOC> ==========================================================================
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@ -342,11 +343,9 @@ aliApses@subject@range@start + aliApses@subject@range@width - 1
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# The following commands should retrieve the correct start and end
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# The following commands should retrieve the correct start and end
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# coordinates and sequence of the MBP1_MYSPE APSES domain:
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# coordinates and sequence of the MBP1_MYSPE APSES domain:
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sel <- myDB$protein$name == paste("MBP1_", biCode(MYSPE), sep = "")
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sel <- which(myDB$protein$name == paste("MBP1_", biCode(MYSPE), sep = ""))
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aaMBP1_MYSPE <- AAString(myDB$protein$sequence[sel])
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(proID <- myDB$protein$ID[sel])
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(proID <- myDB$protein$ID[myDB$protein$name == "MBP1_<MYSSPE>"]) # <<< EDIT
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(ftrID <- myDB$feature$ID[myDB$feature$name == "APSES fold"])
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(ftrID <- myDB$feature$ID[myDB$feature$name == "APSES fold"])
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(fanID <- myDB$annotation$ID[myDB$annotation$proteinID == proID &
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(fanID <- myDB$annotation$ID[myDB$annotation$proteinID == proID &
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myDB$annotation$featureID == ftrID])
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myDB$annotation$featureID == ftrID])
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