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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"
#
# ---------------------------------------------------------------------------- #
# PATIENCE ... #
# Do not yet work wih this code. Updates in progress. Thank you. #
# boris.steipe@utoronto.ca #
# ---------------------------------------------------------------------------- #
#
# Purpose: A Bioinformatics Course:
# 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)
#
# Versions:
# 1.7 2020 updates
# 1.6 Maintenance
# 1.5 Change from require() to requireNamespace(),
# use <package>::<function>() idiom throughout
@ -41,20 +36,20 @@
#TOC> ==========================================================================
#TOC>
#TOC>
#TOC> Section Title Line
#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> 1 Prepare 56
#TOC> 2 Biostrings Pairwise Alignment 73
#TOC> 2.1 Optimal global alignment 91
#TOC> 2.2 Optimal local alignment 154
#TOC> 3 APSES Domain annotation by alignment 178
#TOC> 4 Update your database script 259
#TOC> 4.1 Preparing an annotation file ... 265
#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 310
#TOC> 4.2 Execute and Validate 334
#TOC>
#TOC> ==========================================================================
@ -72,7 +67,7 @@ if (! requireNamespace("seqinr", quietly=TRUE)) {
# You need to recreate the protein database that you have constructed in the
# BIN-Storing_data unit.
source("makeProteinDB.R")
source("./myScripts/makeProteinDB.R")
# = 2 Biostrings Pairwise Alignment =======================================
@ -312,7 +307,7 @@ 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