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hyginn 2020-09-22 21:02:13 +10:00
parent ca0d78c4b9
commit 4c2e911a5a
1 changed files with 18 additions and 21 deletions
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RPR-RegEx.R
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@ -1,19 +1,14 @@
# tocID <- "RPR-RegEx.R" # tocID <- "RPR-RegEx.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 RPR-RegEx unit # R code accompanying the RPR-RegEx unit
# #
# Version: 0.1 # Version: 1.0
# #
# Date: 2017 08 25 # Date: 2017-08 - 2020-09
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# V 0.1 Maintenance 2020
# V 0.1 First code # V 0.1 First code
# #
# TODO: # TODO:
@ -29,22 +24,19 @@
# #
# ============================================================================== # ==============================================================================
#TOC> ========================================================================== #TOC> ==========================================================================
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> ---------------------------------------------- #TOC> ----------------------------------------------------
#TOC> 1 A regex example 44 #TOC> 1 A regex example 41
#TOC> 2 Counting lines 111 #TOC> 2 Counting lines 108
#TOC> 2.1 Counting C-alpha atoms only 128 #TOC> 2.1 Counting C-alpha atoms only 126
#TOC> 3 Code Solutions 144 #TOC> 3 Code Solutions 142
#TOC> 3.1 Counting atoms 146 #TOC> 3.1 Counting atoms 144
#TOC> 3.2 Counting C-alpha records 160 #TOC> 3.2 Counting C-alpha records 160
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
#TOC>
#TOC>
#TOC>
#TOC>
# = 1 A regex example ===================================================== # = 1 A regex example =====================================================
@ -125,7 +117,8 @@ myPDB <- readLines("./data/0TST.pdb")
# Return the number of lines in that file that begin with "ATOM " # Return the number of lines in that file that begin with "ATOM "
# or with "HETATM". # or with "HETATM".
# Try this. Solution code is at the end of this file. Don't peek. # Try this. Write a function. Solution code is at the end of this file.
# Don't peek.
atomCount("./data/0TST.pdb") # must return 6 atomCount("./data/0TST.pdb") # must return 6
@ -157,6 +150,8 @@ atomCount <- function(IN) {
# IN chr path of the file to read # IN chr path of the file to read
# Value: # Value:
# numeric number of lines that match "^ATOM " or "^HETATM" # numeric number of lines that match "^ATOM " or "^HETATM"
# Note: the regex MUST be anchored to the beginning of the line, otherwise
# it might match somewhere in a comment!
x <- readLines(IN) x <- readLines(IN)
patt <- "(^ATOM )|(^HETATM)" patt <- "(^ATOM )|(^HETATM)"
return(length(grep(patt, x))) return(length(grep(patt, x)))
@ -173,6 +168,8 @@ CAcount <- function(IN) {
# Value: # Value:
# numeric number of lines that match " CA " in position 13 - 16 of # numeric number of lines that match " CA " in position 13 - 16 of
# an ATOM record. # an ATOM record.
# Note: the regex MUST be aligned into the right position, otherwise it
# might match Calcium records!
x <- readLines(IN) x <- readLines(IN)
patt <- "^ATOM ...... CA " patt <- "^ATOM ...... CA "
return(length(grep(patt, x))) return(length(grep(patt, x)))