Locked out - Updates needed for 2021

BIN-ALI-BLAST.R

@@ -3,6 +3,22 @@
 # Purpose:  A Bioinformatics Course:
 #              R code accompanying the BIN-ALI-BLAST unit.
 #
+# ==============================================================================
+#
+#                                   S T O P :
+#                                   =========
+#
+#                                     2021
+#                                UPDATE WARNING!
+#                                ---------------
+#
+#  This file has not yet been updated for coursework.  You may inspect it, but
+#  do NOT use it for actual coursework as long as this warning is here.  Parts
+#  of the code and data will change, and if you use this outdated code it will
+#  break your setup and workflow.
+#
+# ==============================================================================
+#
 # Version:  1.3
 #
 # Date:     2017-10  -  2020-09
@@ -30,13 +46,13 @@
 
 
 #TOC> ==========================================================================
-#TOC> 
+#TOC>
 #TOC>   Section  Title                               Line
 #TOC> ---------------------------------------------------
 #TOC>   1        Defining the APSES domain             43
 #TOC>   2        Executing the BLAST search            73
 #TOC>   3        Analysing results                     95
-#TOC> 
+#TOC>
 #TOC> ==========================================================================
 
 

BIN-ALI-Dotplot.R

@@ -1,10 +1,21 @@
 # tocID <- "BIN-ALI-Dotplot.R"
 #
-# ---------------------------------------------------------------------------- #
+#
-#  PATIENCE  ...                                                               #
+# ==============================================================================
-#    Do not yet work wih this code. Updates in progress. Thank you.            #
+#
-#    boris.steipe@utoronto.ca                                                  #
+#                                   S T O P :
-# ---------------------------------------------------------------------------- #
+#                                   =========
+#
+#                                     2021
+#                                UPDATE WARNING!
+#                                ---------------
+#
+#  This file has not yet been updated for coursework.  You may inspect it, but
+#  do NOT use it for actual coursework as long as this warning is here.  Parts
+#  of the code and data will change, and if you use this outdated code it will
+#  break your setup and workflow.
+#
+# ==============================================================================
 #
 # Purpose:  A Bioinformatics Course:
 #              R code accompanying the BIN-ALI-Dotplot unit.

BIN-ALI-MSA.R

@@ -3,6 +3,21 @@
 # Purpose:  A Bioinformatics Course:
 #              R code accompanying the BIN-ALI-MSA unit.
 #
+# ==============================================================================
+#
+#                                   S T O P :
+#                                   =========
+#
+#                                     2021
+#                                UPDATE WARNING!
+#                                ---------------
+#
+#  This file has not yet been updated for coursework.  You may inspect it, but
+#  do NOT use it for actual coursework as long as this warning is here.  Parts
+#  of the code and data will change, and if you use this outdated code it will
+#  break your setup and workflow.
+#
+# ==============================================================================
 # Version:  1.3
 #
 # Date:     2017-10  -  2020-09
@@ -30,7 +45,7 @@
 
 
 #TOC> ==========================================================================
-#TOC> 
+#TOC>
 #TOC>   Section  Title                                              Line
 #TOC> ------------------------------------------------------------------
 #TOC>   1        Preparations                                         55
@@ -48,7 +63,7 @@
 #TOC>   6        Sequence Logos                                      549
 #TOC>   6.1        Subsetting an alignment by motif                  558
 #TOC>   6.2        Plot a Sequence Logo                              607
-#TOC> 
+#TOC>
 #TOC> ==========================================================================
 
 
@@ -241,7 +256,7 @@ for (i in seq_along(highScoringRanges$lengths)) {
 #   -  adjust the sequence names
 #   -  convert to msaAAMultipleAlignment object
 
-# ===   4.1.1  importing an .aln file                   
+# ===   4.1.1  importing an .aln file
 
 # The seqinr package has a function to read CLUSTAL W formatted .aln files ...
 if (! requireNamespace("seqinr", quietly=TRUE)) {

BIN-ALI-Optimal_sequence_alignment.R

@@ -3,6 +3,21 @@
 # Purpose:  A Bioinformatics Course:
 #              R code accompanying the BIN-ALI-Optimal_sequence_alignment unit.
 #
+# ==============================================================================
+#
+#                                   S T O P :
+#                                   =========
+#
+#                                     2021
+#                                UPDATE WARNING!
+#                                ---------------
+#
+#  This file has not yet been updated for coursework.  You may inspect it, but
+#  do NOT use it for actual coursework as long as this warning is here.  Parts
+#  of the code and data will change, and if you use this outdated code it will
+#  break your setup and workflow.
+#
+# ==============================================================================
 # Version:  1.7.1
 #
 # Date:     2017-09   -   2020-10

BIN-FUNC-Domain_annotation.R

@@ -3,6 +3,21 @@
 # Purpose:  A Bioinformatics Course:
 #              R code accompanying the BIN-FUNC-Domain_annotation unit.
 #
+# ==============================================================================
+#
+#                                   S T O P :
+#                                   =========
+#
+#                                     2021
+#                                UPDATE WARNING!
+#                                ---------------
+#
+#  This file has not yet been updated for coursework.  You may inspect it, but
+#  do NOT use it for actual coursework as long as this warning is here.  Parts
+#  of the code and data will change, and if you use this outdated code it will
+#  break your setup and workflow.
+#
+# ==============================================================================
 # Version:  1.4
 #
 # Date:     2017-11  -  2020-10
@@ -31,7 +46,7 @@
 
 
 #TOC> ==========================================================================
-#TOC> 
+#TOC>
 #TOC>   Section  Title                                                 Line
 #TOC> ---------------------------------------------------------------------
 #TOC>   1        Update your database script                             50
@@ -43,7 +58,7 @@
 #TOC>   3        SHARING DATA                                           286
 #TOC>   3.1        Post MBP1_MYSPE as JSON data                         302
 #TOC>   3.2        Import shared MBP1_MYSPE from the Wiki               325
-#TOC> 
+#TOC>
 #TOC> ==========================================================================
 
 
@@ -105,7 +120,7 @@
 # Then SKIP the next section.
 #
 #
-# ===   1.1.2  AFTER "BIN-ALI-Optimal_sequence_alignment"  
+# ===   1.1.2  AFTER "BIN-ALI-Optimal_sequence_alignment"
 #
 #   IF YOU HAVE ALREADY COMPLETED THE BIN-ALI-OPTIMAL_SEQUENCE_ALIGNMENT UNIT:
 #

BIN-MYSPE.R

@@ -3,6 +3,23 @@
 # Purpose: A Bioinformatics Course:
 #              R code accompanying the BIN-MYSPE unit
 #
+# ==============================================================================
+#
+#                                   S T O P :
+#                                   =========
+#
+#                                     2021
+#                                UPDATE WARNING!
+#                                ---------------
+#
+#  This file has not yet been updated for coursework.  You may inspect it, but
+#  do NOT use it for actual coursework as long as this warning is here.  Parts
+#  of the code and data will change, and if you use this outdated code it will
+#  break your setup and workflow.
+#
+# ==============================================================================
+#
+#
 # Version: 1.2
 #
 # Date:    2020-10-01
@@ -31,7 +48,7 @@
 
 
 #TOC> ==========================================================================
-#TOC> 
+#TOC>
 #TOC>   Section  Title                                             Line
 #TOC> -----------------------------------------------------------------
 #TOC>   1        PREPARATIONS                                        49
@@ -42,7 +59,7 @@
 #TOC>   4.2        Visualizing proportions: Pie chart               161
 #TOC>   4.3        Visualizing proportions: Nested squares          238
 #TOC>   4.4        Visualizing proportions: Sankey diagrams         275
-#TOC> 
+#TOC>
 #TOC> ==========================================================================
 
 

FND-STA-Information_theory.R

@@ -1,17 +1,27 @@
 # tocID <- "FND-STA-Information_theory.R"
 #
-# ---------------------------------------------------------------------------- #
+# ==============================================================================
-#  PATIENCE  ...                                                               #
+#
-#    Do not yet work wih this code. Updates in progress. Thank you.            #
+#                                   S T O P :
-#    boris.steipe@utoronto.ca                                                  #
+#                                   =========
-# ---------------------------------------------------------------------------- #
+#
+#                                     2021
+#                                UPDATE WARNING!
+#                                ---------------
+#
+#  This file has not yet been updated for coursework.  You may inspect it, but
+#  do NOT use it for actual coursework as long as this warning is here.  Parts
+#  of the code and data will change, and if you use this outdated code it will
+#  break your setup and workflow.
+#
+# ==============================================================================
 #
 # Purpose:  A Bioinformatics Course:
 #              R code accompanying the FND-STA-Information_theory unit.
 #
 # Version:  0.2.1
 #
-# Date:     2017 - 2019
+# Date:     2017 - 2021
 # Author:   Boris Steipe (boris.steipe@utoronto.ca)
 #
 # Versions:

RPR-GEO2R.R

@@ -3,6 +3,22 @@
 # Purpose:  A Bioinformatics Course:
 #              R code accompanying the RPR_GEO2R unit.
 #
+#
+# ==============================================================================
+#
+#                                   S T O P :
+#                                   =========
+#
+#                                     2021
+#                                UPDATE WARNING!
+#                                ---------------
+#
+#  This file has not yet been updated for coursework.  You may inspect it, but
+#  do NOT use it for actual coursework as long as this warning is here.  Parts
+#  of the code and data will change, and if you use this outdated code it will
+#  break your setup and workflow.
+#
+# ==============================================================================
 # Version:  1.3
 #
 # Date:     2017-09  -  2020-09
@@ -292,6 +308,9 @@ readLines("./data/SGD_features.tab", n = 5)
 
 # ==   4.1  Task - Read a table of features  ===================================
 
+#      Note: this task asks you to write code. You MUST identify your
+#      sources when you draw on other's examples.
+
 # This data file is rather typical of datasets that you will encounter "in the
 # wild". To proceed, you need to write code to read it into an R-object. Develop
 # the code in your script file according to the following specification: