update validateFASTA() logic to accommodate blanks in spacers
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hyginn
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169ca58b92
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092494d9de
85
.utilities.R
85
.utilities.R
@ -20,7 +20,7 @@
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#TOC> ==========================================================================
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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 SCRIPTS TO SOURCE 50
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@ -43,7 +43,7 @@
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#TOC> 5.03 selectPDBrep() 438
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#TOC> 5.04 selectChi2() 474
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#TOC> 5.05 selectENSP() 487
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#TOC>
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#TOC>
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#TOC> ==========================================================================
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@ -206,6 +206,7 @@ validateFA <- function(txt) {
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#
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# The function is used for its side-effect of throwing an error of
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# FASTA assumptions are violated in txt.
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# - There may be spacer-lines matching "^\\s*$"
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# - At least one header line
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# - No adjacent header lines
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# - All header lines followed by at least one sequence line
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@ -216,34 +217,92 @@ validateFA <- function(txt) {
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stop("no header lines in input")
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}
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sel <- grepl("^>", txt)
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sel <- sel[- length(sel)] & sel[-1]
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isHeader <- grepl("^>", txt)
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isSpacer <- grepl("^\\s*$", txt)
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txtNoSpc <- txt[! isSpacer]
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# adjacent headers
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sel <- isHeader[- length(isHeader)] & isHeader[-1]
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if ( any(sel) ) {
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i <- which(sel)[1]
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stop(sprintf("adjacent header lines in input (lines %d and %d)",
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i, i+1))
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}
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selA <- grepl("^>", txt)
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# invalid character in a line that is not header or spacer
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selA <- isHeader | isSpacer
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selB <- grepl(sprintf("[^%s]", AAVALID), txt)
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if ( any( (! selA) & selB) ) { # (not header) AND (has invalid character)
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i <- which( (! selA) & selB)[1]
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stop(sprintf("invalid character(s) in sequence (cf. line %d)",
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i, i+1))
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stop(sprintf("invalid character(s) in sequence (cf. line %d)", i))
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}
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sel <- grep("^>", txt) + 1
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sel <- grepl(sprintf("[%s]+", AAVALID), txt[sel])
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if ( ! all(sel) ) {
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i <- which( ! sel)[1]
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stop(sprintf("a header has no adjacent sequence (line %d)",
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grep("^>", txt)[i]))
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# no spacer should immediately follow a header
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sel <- c(isSpacer, FALSE) & c(FALSE, isHeader)
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if ( any(sel) ) {
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i <- which(sel)[1]
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stop(sprintf("a header has no adjacent sequence (line %d)", i - 1))
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}
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# no header alone on the last line
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if ( which(isHeader)[sum(isHeader)] == length(txt)) {
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stop(sprintf("a header is alone on the last line (line %d)", length(txt)))
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}
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# no spacer in a block of sequence
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# (tested as: not followed by spacer or header)
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if (sum(isSpacer) > 0) {
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sel <- which(isSpacer) + 1
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sel <- sel[sel <= length(txt)]
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if ( ! all(isSpacer[sel] | isHeader[sel]) ) {
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i <- which(! (isSpacer[sel] | isHeader[sel]))[1]
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stop(sprintf("a spacer is followed by sequence (line %d)",
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which(isSpacer)[i]))
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}
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}
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# all good, if we get to here.
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return(invisible(NULL))
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}
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if (FALSE) {
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# Should validate
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fa <- c(">abc", "de")
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validateFA(fa)
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fa <- c(">abc", "de", "fgh", ">ojz", "ikl")
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validateFA(fa)
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fa <- c("", ">abc", "de", "fgh", "", ">ojz", "ikl", "")
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validateFA(fa)
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fa <- c(" ", ">abc", "de", "fgh", " ", ">ojz", "ikl", "\t")
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validateFA(fa)
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# should fail
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fa <- c("abc", "de")
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validateFA(fa)
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fa <- c(">abc", "de", ">fgh", ">ojz", "ikl")
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validateFA(fa)
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fa <- c("", ">abc", "de", "f_h", "", ">ojz", "ikl", "")
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validateFA(fa)
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fa <- c(">abc", " ", "de", "fgh", " ", ">ojz", "ikl", "\t")
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validateFA(fa)
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fa <- c(" ", ">abc", "de", "fgh", " ", ">ojz")
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validateFA(fa)
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fa <- c(" ", ">abc", "de", " ", "fgh", ">ojz", "ikl", "\t")
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validateFA(fa)
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}
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# == 4.05 readFASTA() ======================================================
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11
RPR-FASTA.R
11
RPR-FASTA.R
@ -32,8 +32,8 @@
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#TOC>
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#TOC> Section Title Line
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#TOC> -----------------------------------------------------
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#TOC> 1 Reading and validating FASTA 45
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#TOC> 1.1 Validating FASTA 81
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#TOC> 1 Reading and validating FASTA 44
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#TOC> 1.1 Validating FASTA 80
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#TOC> 2 Parsing FASTA 225
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#TOC> 3 Interpreting FASTA 245
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#TOC> 4 Writing FASTA 272
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@ -218,8 +218,9 @@ FA <- c(">head1",
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validate(FA) # ... should not create an error
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# a somewhat more elaborate validateFA() function was loaded with the
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# ./utilities.R script
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# A somewhat more elaborate validateFA() function was loaded with the
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# ./utilities.R script. It needs a bit more bookkeeping, since NCBI multi-
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# fasta files have space-characters in their spacer lines.
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# = 2 Parsing FASTA =======================================================
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@ -271,7 +272,7 @@ pie(table(x)[names(AACOLS)], col = AACOLS)
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# = 4 Writing FASTA =======================================================
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# Writing FASTA files mostly just the revrese reverse of reading, with one
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# Writing FASTA files is mostly just the reverse of reading, with one
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# twist: we need to break the long sequence string into chunks of the desired
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# width. The FASTA specification calls for a maximum of 120 characters per line,
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# but writing out much less than that is common, since it allows to comfortably
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