From 12725799e149c302c02e2d4394da5a800f14ba70 Mon Sep 17 00:00:00 2001 From: hyginn Date: Sat, 26 Sep 2020 16:45:29 +1000 Subject: [PATCH] Maintenance --- BIN-PHYLO-Data_preparation.R | 43 ++++++++++++++++-------------------- 1 file changed, 19 insertions(+), 24 deletions(-) diff --git a/BIN-PHYLO-Data_preparation.R b/BIN-PHYLO-Data_preparation.R index 382817d..407faff 100644 --- a/BIN-PHYLO-Data_preparation.R +++ b/BIN-PHYLO-Data_preparation.R @@ -1,20 +1,15 @@ # tocID <- "BIN-PHYLO-Data_preparation.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-PHYLO-Data_preparation unit. # -# Version: 1.1 +# Version: 1.2 # -# Date: 2017 10 - 2019 01 +# Date: 2017-10 - 2020-09 # Author: Boris Steipe (boris.steipe@utoronto.ca) # # Versions: +# 1.2 2020 Maintenance # 1.1 Change from require() to requireNamespace(), # use ::() idiom throughout, # use Biocmanager:: not biocLite() @@ -35,15 +30,15 @@ #TOC> ========================================================================== -#TOC> +#TOC> #TOC> Section Title Line #TOC> --------------------------------------------------------- -#TOC> 1 Preparations 44 -#TOC> 2 Fetching sequences 76 -#TOC> 3 Multiple Sequence Alignment 117 -#TOC> 4 Reviewing and Editing Alignments 136 -#TOC> 4.1 Masking workflow 152 -#TOC> +#TOC> 1 Preparations 45 +#TOC> 2 Fetching sequences 77 +#TOC> 3 Multiple Sequence Alignment 118 +#TOC> 4 Reviewing and Editing Alignments 137 +#TOC> 4.1 Masking workflow 153 +#TOC> #TOC> ========================================================================== @@ -54,7 +49,7 @@ # been made to the reference files. If you have worked with the prerequiste # units, you should have a script named "makeProteinDB.R" that will create the # myDB object with a protein and feature database. Ask for advice if not. -source("makeProteinDB.R") +source("myScripts/makeProteinDB.R") # Load packages we need @@ -172,16 +167,16 @@ for (i in 1:nrow(APSESMsa)) { } # inspect the result -msaMatrix[1:7, 1:14] +msaMatrix[1:7, 30:40] # Now let's make a logical vector with an element for each column that selects # which columns should be masked out. # The number of hyphens in a column is easy to count. Consider: - msaMatrix[ , 20] - msaMatrix[ , 20] == "-" -sum(msaMatrix[ , 20] == "-") + msaMatrix[ , 20] # column 20 + msaMatrix[ , 20] == "-" # TRUE for all gap characters +sum(msaMatrix[ , 20] == "-") # adds 1 for each TRUE # Thus filling our logical vector is simple: @@ -192,7 +187,7 @@ colMask <- logical(ncol(msaMatrix)) limit <- round(nrow(APSESMsa) * (2/3)) # iterate over all columns, and write TRUE if there are less-or-equal to "limit" -# hyphens, FALSE if there are more - i.e. TRUE columns will be used fr analysis +# hyphens, FALSE if there are more - i.e. TRUE columns will be used for analysis # and FALSE columns will be rejected. for (i in 1:ncol(msaMatrix)) { count <- sum(msaMatrix[ , i] == "-") @@ -230,9 +225,9 @@ writeALN(APSESphyloSet) # several indels from the KILA_ESCCO outgroup sequence. -# We save the aligned, masked domains to a file in multi-FASTA format. -writeMFA(APSESphyloSet, myCon = "APSESphyloSet.mfa") - +# We save the aligned, masked domains to a file in the data/ directory, +# in multi-FASTA format. +writeMFA(APSESphyloSet, myCon = "data/APSESphyloSet.mfa")