From 9143b784e9adb6149676329f1b8c0377e4dee0ee Mon Sep 17 00:00:00 2001 From: hyginn Date: Thu, 16 Sep 2021 01:29:19 -0400 Subject: [PATCH] Locked out - Updates needed for 2021 --- BIN-ALI-BLAST.R | 20 ++++++++++++++++++-- BIN-ALI-Dotplot.R | 21 ++++++++++++++++----- BIN-ALI-MSA.R | 21 ++++++++++++++++++--- BIN-ALI-Optimal_sequence_alignment.R | 15 +++++++++++++++ BIN-FUNC-Domain_annotation.R | 21 ++++++++++++++++++--- BIN-MYSPE.R | 21 +++++++++++++++++++-- FND-STA-Information_theory.R | 22 ++++++++++++++++------ RPR-GEO2R.R | 19 +++++++++++++++++++ 8 files changed, 139 insertions(+), 21 deletions(-) diff --git a/BIN-ALI-BLAST.R b/BIN-ALI-BLAST.R index 191ca5f..4a6cc3f 100644 --- a/BIN-ALI-BLAST.R +++ b/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 Parts +# of the code and data will change, and if you use this outdated code it will +# break your setup and workflow.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> ========================================================================== diff --git a/BIN-ALI-Dotplot.R b/BIN-ALI-Dotplot.R index 661cdde..56ce80e 100644 --- a/BIN-ALI-Dotplot.R +++ b/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. diff --git a/BIN-ALI-MSA.R b/BIN-ALI-MSA.R index 0265d21..0d9f7dc 100644 --- a/BIN-ALI-MSA.R +++ b/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)) { diff --git a/BIN-ALI-Optimal_sequence_alignment.R b/BIN-ALI-Optimal_sequence_alignment.R index b981f05..27a26e8 100644 --- a/BIN-ALI-Optimal_sequence_alignment.R +++ b/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 diff --git a/BIN-FUNC-Domain_annotation.R b/BIN-FUNC-Domain_annotation.R index c45e833..6f7750d 100644 --- a/BIN-FUNC-Domain_annotation.R +++ b/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: # diff --git a/BIN-MYSPE.R b/BIN-MYSPE.R index 84bbb82..595d1f1 100644 --- a/BIN-MYSPE.R +++ b/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> ========================================================================== diff --git a/FND-STA-Information_theory.R b/FND-STA-Information_theory.R index 3161bad..0dd0aa2 100644 --- a/FND-STA-Information_theory.R +++ b/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. # -# 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 FND-STA-Information_theory unit. # # Version: 0.2.1 # -# Date: 2017 - 2019 +# Date: 2017 - 2021 # Author: Boris Steipe (boris.steipe@utoronto.ca) # # Versions: diff --git a/RPR-GEO2R.R b/RPR-GEO2R.R index 25adc8d..85f9e1c 100644 --- a/RPR-GEO2R.R +++ b/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: