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Update script location

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hyginn 2020-09-25 21:50:42 +10:00
parent 092daaef97
commit 091880d205
1 changed files with 19 additions and 16 deletions
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31
BIN-ALI-BLAST.R
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@ -1,20 +1,15 @@
# tocID <- "BIN-ALI-BLAST.R" # tocID <- "BIN-ALI-BLAST.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-BLAST unit. # R code accompanying the BIN-ALI-BLAST unit.
# #
# Version: 1.2 # Version: 1.3
# #
# Date: 2017 10 - 2019 01 # Date: 2017-10 - 2020-09
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 1.3 2020 Maintenance
# 1.2 Change from require() to requireNamespace(), # 1.2 Change from require() to requireNamespace(),
# use <package>::<function>() idiom throughout # use <package>::<function>() idiom throughout
# 1.1 Fixed parsing logic. # 1.1 Fixed parsing logic.
@ -38,9 +33,9 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> --------------------------------------------------- #TOC> ---------------------------------------------------
#TOC> 1 Defining the APSES domain 42 #TOC> 1 Defining the APSES domain 43
#TOC> 2 Executing the BLAST search 64 #TOC> 2 Executing the BLAST search 73
#TOC> 3 Analysing results 86 #TOC> 3 Analysing results 95
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -50,10 +45,18 @@
# Load your protein database # Load your protein database
source("makeProteinDB.R") source("makeProteinDB.R")
# Get the APSES domain sequence for MBP1_MYSPE feature annotation. (You have # Get the APSES domain sequence via your MBP1_MYSPE feature annotation. (You
# entered this data in the BIN-ALI-Optimal_sequence_alignment unit.) # have entered this data into your database in the
# BIN-ALI-Optimal_sequence_alignment unit.)
(proID <- myDB$protein$ID[myDB$protein$name == "MBP1_<MYSSPE>"]) # <<< EDIT ( myOrth <- sprintf("MBP1_%s", biCode(MYSPE)) ) # If this is not the correct
# name of the Mbp1 orthologue
# of Mbp1 in your protein
# database, DON'T continue. We
# need to fix this problem.
# Get in touch.
(proID <- myDB$protein$ID[myDB$protein$name == myOrth])
(ftrID <- myDB$feature$ID[myDB$feature$name == "APSES fold"]) (ftrID <- myDB$feature$ID[myDB$feature$name == "APSES fold"])
(fanID <- myDB$annotation$ID[myDB$annotation$proteinID == proID & (fanID <- myDB$annotation$ID[myDB$annotation$proteinID == proID &
myDB$annotation$featureID == ftrID]) myDB$annotation$featureID == ftrID])