184 lines
6.7 KiB
R
184 lines
6.7 KiB
R
# tocID <- "RPR-RegEx.R"
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#
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# ---------------------------------------------------------------------------- #
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# PATIENCE ... #
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# Do not yet work wih this code. Updates in progress. Thank you. #
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# boris.steipe@utoronto.ca #
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# ---------------------------------------------------------------------------- #
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#
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# Purpose: A Bioinformatics Course:
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# R code accompanying the RPR-RegEx unit
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#
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# Version: 0.1
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#
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# Date: 2017 08 25
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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#
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# V 0.1 First code
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#
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# TODO:
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#
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#
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# == HOW TO WORK WITH LEARNING UNIT FILES ======================================
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#
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# DO NOT SIMPLY source() THESE FILES!
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#
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# If there are portions you don't understand, use R's help system, Google for an
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# answer, or ask your instructor. Don't continue if you don't understand what's
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# going on. That's not how it works ...
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#
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# ==============================================================================
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#TOC> ==========================================================================
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#TOC>
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#TOC> Section Title Line
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#TOC> ----------------------------------------------
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#TOC> 1 A regex example 44
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#TOC> 2 Counting lines 111
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#TOC> 2.1 Counting C-alpha atoms only 128
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#TOC> 3 Code Solutions 144
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#TOC> 3.1 Counting atoms 146
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#TOC> 3.2 Counting C-alpha records 160
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#TOC>
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#TOC> ==========================================================================
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#TOC>
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#TOC>
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#TOC>
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#TOC>
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# = 1 A regex example =====================================================
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# The canonical FASTA version of yeast Mbp1 at Uniprot
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s <- ">sp|P39678|MBP1_YEAST Transcription factor MBP1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MBP1 PE=1 SV=1
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MSNQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLK
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ETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASPPPAPKHHHA
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SKVDRKKAIRSASTSAIMETKRNNKKAEENQFQSSKILGNPTAAPRKRGRPVGSTRGSRR
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KLGVNLQRSQSDMGFPRPAIPNSSISTTQLPSIRSTMGPQSPTLGILEEERHDSRQQQPQ
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QNNSAQFKEIDLEDGLSSDVEPSQQLQQVFNQNTGFVPQQQSSLIQTQQTESMATSVSSS
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PSLPTSPGDFADSNPFEERFPGGGTSPIISMIPRYPVTSRPQTSDINDKVNKYLSKLVDY
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FISNEMKSNKSLPQVLLHPPPHSAPYIDAPIDPELHTAFHWACSMGNLPIAEALYEAGTS
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IRSTNSQGQTPLMRSSLFHNSYTRRTFPRIFQLLHETVFDIDSQSQTVIHHIVKRKSTTP
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SAVYYLDVVLSKIKDFSPQYRIELLLNTQDKNGDTALHIASKNGDVVFFNTLVKMGALTT
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ISNKEGLTANEIMNQQYEQMMIQNGTNQHVNSSNTDLNIHVNTNNIETKNDVNSMVIMSP
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VSPSDYITYPSQIATNISRNIPNVVNSMKQMASIYNDLHEQHDNEIKSLQKTLKSISKTK
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IQVSLKTLEVLKESSKDENGEAQTNDDFEILSRLQEQNTKKLRKRLIRYKRLIKQKLEYR
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QTVLLNKLIEDETQATTNNTVEKDNNTLERLELAQELTMLQLQRKNKLSSLVKKFEDNAK
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IHKYRRIIREGTEMNIEEVDSSLDVILQTLIANNNKNKGAEQIITISNANSHA"
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nchar(s)
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# Must be 969
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# Task: Fetch the Uniprot ID by retrieving the first string that appears between
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# two vertical bars ("pipes") in the header record.
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#
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# Develop the regular expression:
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# Just five characters returned, so we know we are using
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patt <- "^>(.{5})" # the right functions
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regmatches(s, regexec(patt, s, perl = TRUE))[[1]][2]
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patt <- "^>(.*)|" # everything to the pipe character
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regmatches(s, regexec(patt, s, perl = TRUE))[[1]][2]
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# Ooops - "|" is a metacharacter - we must escape it
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patt <- "^>(.*)\|" # using "\|"
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# Ooops - that's not how we escape: must double the \ to send a literal
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# "\" plus the character "|" to the regex engine.
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patt <- "^>(.*)\\|" # using "\\|"
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regmatches(s, regexec(patt, s, perl = TRUE))[[1]][2]
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# Good. Now let's first match everything that is not a "|", then match a "|"
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patt <- "^>([^|]*)\\|"
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regmatches(s, regexec(patt, s, perl = TRUE))[[1]][2]
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# the same thing again, but capture the second match. And insist that there
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# must be at least one character captured
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patt <- "^>[^|]*\\|([^|]+)\\|"
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# Analyze this pattern:
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# ^ anchor the match at the beginning of the line
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# > ">" must be the first character
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# [^|]* all-characters-except-a-vertical-bar, 0 or more times because
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# we don't know what other versions of the string "sp"
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# might appear. Note that within the brackets "|" is NOT a
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# metacharacter.
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# \\| "|" character: ouside of square brackets "|" is a metacharacter
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# and means "OR"; we need to escape it to match a literal "|".
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# ( open parenthesis: capture what comes next ...
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# [^|]+ all-characters-except-a-vertical-bar, 1 or more times
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# ) close parenthesis: stop capturing here
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# \\| second "|" character, escaped
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regmatches(s, regexec(patt, s, perl = TRUE))[[1]][2]
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# = 2 Counting lines ======================================================
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# Task: Write a function that returns the number of atoms in a PDB file. Call it
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# atomCount(). Sample data is here:
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myPDB <- readLines("./data/0TST.pdb")
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# Specification:
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# Read a file from its path given as the only argument.
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# Return the number of lines in that file that begin with "ATOM "
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# or with "HETATM".
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# Try this. Solution code is at the end of this file. Don't peek.
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atomCount("./data/0TST.pdb") # must return 6
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# == 2.1 Counting C-alpha atoms only =======================================
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# Task: write a function based on the previous one that matches only CA records,
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# i.e. it can be used to count the number of amino acids. Don't get
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# fooled by calcium atoms, or the string CA appearing elsewhere.
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# cf. https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
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# Specification:
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# Read a file from its path given as the only argument.
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# Return the number of lines in that file that have a C-alpha atom.
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# Try this. Solution code is at the end of this file. Don't peek.
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CAcount("./data/0TST.pdb") # must return 1
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# = 3 Code Solutions ======================================================
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# == 3.1 Counting atoms ====================================================
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atomCount <- function(IN) {
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# count the number of atoms in a PDB formatted file
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# Parameters:
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# IN chr path of the file to read
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# Value:
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# numeric number of lines that match "^ATOM " or "^HETATM"
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x <- readLines(IN)
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patt <- "(^ATOM )|(^HETATM)"
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return(length(grep(patt, x)))
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}
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# == 3.2 Counting C-alpha records ==========================================
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CAcount <- function(IN) {
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# count the number of C-alpha atoms in a PDB formatted file
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# Parameters:
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# IN chr path of the file to read
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# Value:
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# numeric number of lines that match " CA " in position 13 - 16 of
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# an ATOM record.
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x <- readLines(IN)
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patt <- "^ATOM ...... CA "
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return(length(grep(patt, x)))
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}
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# [END]
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