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Fix makeProteinDB.R location

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hyginn 2020-09-25 21:28:17 +10:00
parent 126f956ea7
commit 092daaef97
1 changed files with 17 additions and 22 deletions
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39
BIN-ALI-Optimal_sequence_alignment.R
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@ -1,20 +1,15 @@
# tocID <- "BIN-ALI-Optimal_sequence_alignment.R" # tocID <- "BIN-ALI-Optimal_sequence_alignment.R"
# #
# ---------------------------------------------------------------------------- #
# PATIENCE ... #
# Do not yet work wih this code. Updates in progress. Thank you. #
# boris.steipe@utoronto.ca #
# ---------------------------------------------------------------------------- #
#
# 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: 1.6 # Version: 1.7
# #
# Date: 2017 09 - 2019 11 # Date: 2017-09 - 2020-09
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 1.7 2020 updates
# 1.6 Maintenance # 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
@ -41,20 +36,20 @@
#TOC> ========================================================================== #TOC> ==========================================================================
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> -------------------------------------------------------------------------- #TOC> --------------------------------------------------------------------------
#TOC> 1 Prepare 55 #TOC> 1 Prepare 56
#TOC> 2 Biostrings Pairwise Alignment 72 #TOC> 2 Biostrings Pairwise Alignment 73
#TOC> 2.1 Optimal global alignment 90 #TOC> 2.1 Optimal global alignment 91
#TOC> 2.2 Optimal local alignment 153 #TOC> 2.2 Optimal local alignment 154
#TOC> 3 APSES Domain annotation by alignment 177 #TOC> 3 APSES Domain annotation by alignment 178
#TOC> 4 Update your database script 258 #TOC> 4 Update your database script 259
#TOC> 4.1 Preparing an annotation file ... 264 #TOC> 4.1 Preparing an annotation file ... 265
#TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 266 #TOC> 4.1.1 If you HAVE NOT done the BIN-FUNC-Annotation unit 267
#TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 309 #TOC> 4.1.2 If you HAVE done the BIN-FUNC-Annotation unit 310
#TOC> 4.2 Execute and Validate 333 #TOC> 4.2 Execute and Validate 334
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -72,7 +67,7 @@ if (! requireNamespace("seqinr", quietly=TRUE)) {
# You need to recreate the protein database that you have constructed in the # You need to recreate the protein database that you have constructed in the
# BIN-Storing_data unit. # BIN-Storing_data unit.
source("makeProteinDB.R") source("./myScripts/makeProteinDB.R")
# = 2 Biostrings Pairwise Alignment ======================================= # = 2 Biostrings Pairwise Alignment =======================================
@ -312,7 +307,7 @@ aliApses@subject@range@start + aliApses@subject@range@width - 1
# Then SKIP the next section. # 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 # You DO already have a file called "<MYSPE>-Annotations.json" in the