a possible bug of trimLRPatterns
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wang peter ★ 2.0k
@wang-peter-4647
Last seen 10.2 years ago
reads <- readFastq(fastqfile); seqs <- sread(reads); max.mismatchs <- mismatch_rate*1:nchar(DNAString(PCR2rc)) trimmedCoords <- trimLRPatterns(Rpattern = PCR2rc, subject = seqs, max.Rmismatch= max.mismatchs, with.Rindels=T,ranges=T) > end(trimmedCoords)[1:20] [1] 22 18 20 33 14 22 22 20 22 22 22 15 20 37 19 13 20 22 0 34 > start(trimmedCoords)[1:20] [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 there is a "0" in the end of trimmedCoords so i cannot get the trimmed sequences trimmed3End <- narrow(reads, start=end(trimmedCoords), end=width(reads)) R version 2.14.1 (2011-12-22) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.12.4 latticeExtra_0.6-19 RColorBrewer_1.0-5 [4] Rsamtools_1.6.3 lattice_0.20-0 Biostrings_2.22.0 [7] GenomicRanges_1.6.7 IRanges_1.12.6 loaded via a namespace (and not attached): [1] Biobase_2.14.0 bitops_1.0-4.1 BSgenome_1.22.0 grid_2.14.1 [5] hwriter_1.3 RCurl_1.91-1 rtracklayer_1.14.4 tools_2.14.1 [9] XML_3.9-4 zlibbioc_1.0.0 -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253
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@martin-morgan-1513
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On 03/08/2012 04:40 PM, wang peter wrote: > reads<- readFastq(fastqfile); > seqs<- sread(reads); > max.mismatchs<- mismatch_rate*1:nchar(DNAString(PCR2rc)) > trimmedCoords<- trimLRPatterns(Rpattern = PCR2rc, subject = seqs, > max.Rmismatch= max.mismatchs, with.Rindels=T,ranges=T) > >> end(trimmedCoords)[1:20] > [1] 22 18 20 33 14 22 22 20 22 22 22 15 20 37 19 13 20 22 0 34 >> start(trimmedCoords)[1:20] > [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > > there is a "0" in the end of trimmedCoords so i cannot get the trimmed sequences The sequence has been trimmed entirely > as.character(Views(DNAString("AA"), IRanges(1, 1))) [1] "A" > as.character(Views(DNAString("AA"), IRanges(1, 0))) [1] "" Martin > > trimmed3End<- narrow(reads, start=end(trimmedCoords), end=width(reads)) > > R version 2.14.1 (2011-12-22) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ShortRead_1.12.4 latticeExtra_0.6-19 RColorBrewer_1.0-5 > [4] Rsamtools_1.6.3 lattice_0.20-0 Biostrings_2.22.0 > [7] GenomicRanges_1.6.7 IRanges_1.12.6 > > loaded via a namespace (and not attached): > [1] Biobase_2.14.0 bitops_1.0-4.1 BSgenome_1.22.0 grid_2.14.1 > [5] hwriter_1.3 RCurl_1.91-1 rtracklayer_1.14.4 tools_2.14.1 > [9] XML_3.9-4 zlibbioc_1.0.0 > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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A reply to a similar post also described removal of zero width reads; "If you want to remove zero-width records before writing, then subset as xx[width(xx) != 0]" So in your case something like; nonZero <- (width(trimmedCoords)!=0) narrow(reads[nonZero], start=start(trimmedCoords)[nonZero], end=end(trimmedCoords)[nonZero]) Marcus On Sat, Mar 10, 2012 at 12:10 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 03/08/2012 04:40 PM, wang peter wrote: > >> reads<- readFastq(fastqfile); >> seqs<- sread(reads); >> max.mismatchs<- mismatch_rate*1:nchar(**DNAString(PCR2rc)) >> trimmedCoords<- trimLRPatterns(Rpattern = PCR2rc, subject = seqs, >> max.Rmismatch= max.mismatchs, with.Rindels=T,ranges=T) >> >> end(trimmedCoords)[1:20] >>> >> [1] 22 18 20 33 14 22 22 20 22 22 22 15 20 37 19 13 20 22 0 34 >> >>> start(trimmedCoords)[1:20] >>> >> [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 >> >> there is a "0" in the end of trimmedCoords so i cannot get the trimmed >> sequences >> > > The sequence has been trimmed entirely > > > as.character(Views(DNAString("**AA"), IRanges(1, 1))) > [1] "A" > > as.character(Views(DNAString("**AA"), IRanges(1, 0))) > [1] "" > > Martin > > > >> trimmed3End<- narrow(reads, start=end(trimmedCoords), end=width(reads)) >> >> R version 2.14.1 (2011-12-22) >> Platform: x86_64-redhat-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] ShortRead_1.12.4 latticeExtra_0.6-19 RColorBrewer_1.0-5 >> [4] Rsamtools_1.6.3 lattice_0.20-0 Biostrings_2.22.0 >> [7] GenomicRanges_1.6.7 IRanges_1.12.6 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.14.0 bitops_1.0-4.1 BSgenome_1.22.0 grid_2.14.1 >> [5] hwriter_1.3 RCurl_1.91-1 rtracklayer_1.14.4 tools_2.14.1 >> [9] XML_3.9-4 zlibbioc_1.0.0 >> >> > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
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An srFilter could be useful for filtering reads based on width using the subset operation, the advantage is that you can quickly retrieve statistics from the filter to put in a log file. The output is in the style of 'occurrenceFilter' which uses 'ShortRead:::.occurrenceName' to construct input arguments in the stats summary, other filters don't necessarily include input arguments depending on when they were written. widthFilter <- function (w, .name = .widthName(w)) { ShortRead:::.check_type_and_length(w, "numeric", 1L) if(w < 1) .throw(SRError("UserArgumentMismatch", "'w' must be >= 1'")) srFilter(function(x) { width(x)>=w }, name = .name) } .widthName <- function (w) { sprintf("%s w=%s", "widthFilter", w) } ## Example sp <- SolexaPath(system.file('extdata', package='ShortRead')) rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt") ## Create some variable width reads, note: escaping the backslash rfq.ex <- trimEnds(rfq, "\\") ## e.g. Filter reads at least 20 nucleotide cycles wFilter <- widthFilter(20L) rfq.ex[wFilter(rfq.ex)] ## Output for a log file stats(wFilter(rfq.ex)) stats(!wFilter(rfq.ex)) Name Input Passing Op 1 widthFilter w=20 256 251 <na> 2 !(widthFilter w=20) 256 5 ! Marcus On Sat, Mar 10, 2012 at 11:00 AM, Marcus Davy <mdavy86@gmail.com> wrote: > A reply to a similar post also described removal of zero width reads; > > "If you want to remove zero-width records before writing, then subset as > > xx[width(xx) != 0]" > > So in your case something like; > > nonZero <- (width(trimmedCoords)!=0) > narrow(reads[nonZero], start=start(trimmedCoords)[nonZero], > end=end(trimmedCoords)[nonZero]) > > Marcus > > > On Sat, Mar 10, 2012 at 12:10 AM, Martin Morgan <mtmorgan@fhcrc.org>wrote: > >> On 03/08/2012 04:40 PM, wang peter wrote: >> >>> reads<- readFastq(fastqfile); >>> seqs<- sread(reads); >>> max.mismatchs<- mismatch_rate*1:nchar(**DNAString(PCR2rc)) >>> trimmedCoords<- trimLRPatterns(Rpattern = PCR2rc, subject = seqs, >>> max.Rmismatch= max.mismatchs, with.Rindels=T,ranges=T) >>> >>> end(trimmedCoords)[1:20] >>>> >>> [1] 22 18 20 33 14 22 22 20 22 22 22 15 20 37 19 13 20 22 0 34 >>> >>>> start(trimmedCoords)[1:20] >>>> >>> [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 >>> >>> there is a "0" in the end of trimmedCoords so i cannot get the trimmed >>> sequences >>> >> >> The sequence has been trimmed entirely >> >> > as.character(Views(DNAString("**AA"), IRanges(1, 1))) >> [1] "A" >> > as.character(Views(DNAString("**AA"), IRanges(1, 0))) >> [1] "" >> >> Martin >> >> >> >>> trimmed3End<- narrow(reads, start=end(trimmedCoords), end=width(reads)) >>> >>> R version 2.14.1 (2011-12-22) >>> Platform: x86_64-redhat-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=C LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] ShortRead_1.12.4 latticeExtra_0.6-19 RColorBrewer_1.0-5 >>> [4] Rsamtools_1.6.3 lattice_0.20-0 Biostrings_2.22.0 >>> [7] GenomicRanges_1.6.7 IRanges_1.12.6 >>> >>> loaded via a namespace (and not attached): >>> [1] Biobase_2.14.0 bitops_1.0-4.1 BSgenome_1.22.0 grid_2.14.1 >>> [5] hwriter_1.3 RCurl_1.91-1 rtracklayer_1.14.4 >>> tools_2.14.1 >>> [9] XML_3.9-4 zlibbioc_1.0.0 >>> >>> >> >> -- >> Computational Biology >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> >> Location: M1-B861 >> Telephone: 206 667-2793 >> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > [[alternative HTML version deleted]]
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Slight bug in width checking, .throw is in the ShortRead package. if(w < 1) ShortRead:::.throw(SRError("UserArgumentMismatch", "'w' must be >= 1'")) ## w=0 throws an error widthFilter(0L) Error: UserArgumentMismatch 'w' must be >= 1' wFilter <- widthFilter(1L) ## Negate the operator to check for 0 length reads zeroLength <- (!wFilter(rfq.ex)) rfq.ex[zeroLength] class: ShortReadQ length: 4 reads; width: 0 cycles Marcus On Sun, Mar 18, 2012 at 11:21 AM, Marcus Davy <mdavy86@gmail.com> wrote: > An srFilter could be useful for filtering reads based on width using the > subset operation, the advantage is that you can quickly retrieve statistics > from the filter to put in a log file. > > The output is in the style of 'occurrenceFilter' which uses > 'ShortRead:::.occurrenceName' to construct input arguments in the stats > summary, other filters don't necessarily include input arguments depending > on when they were written. > > > > > widthFilter <- > > > function (w, .name = .widthName(w)) > > > { > > > ShortRead:::.check_type_and_length(w, "numeric", 1L) > > > if(w < 1) > > > .throw(SRError("UserArgumentMismatch", "'w' must be >= 1'")) > > > > > > srFilter(function(x) { > > > width(x)>=w > > > }, name = .name) > > > } > > > > > > .widthName <- function (w) > > > { > > > sprintf("%s w=%s", "widthFilter", w) > > > } > > > > ## Example > > > sp <- SolexaPath(system.file('extdata', package='ShortRead')) > > > rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt") > > > > ## Create some variable width reads, note: escaping the backslash > > > rfq.ex <- trimEnds(rfq, "\\") > > ## e.g. Filter reads at least 20 nucleotide cycles > > > wFilter <- widthFilter(20L) > > > rfq.ex[wFilter(rfq.ex)] > > > > ## Output for a log file > > > stats(wFilter(rfq.ex)) > > > stats(!wFilter(rfq.ex)) > > > > Name Input Passing Op > 1 widthFilter w=20 256 251 <na> > 2 !(widthFilter w=20) 256 5 ! > > > Marcus > > > On Sat, Mar 10, 2012 at 11:00 AM, Marcus Davy <mdavy86@gmail.com> wrote: > >> A reply to a similar post also described removal of zero width reads; >> >> "If you want to remove zero-width records before writing, then subset as >> >> xx[width(xx) != 0]" >> >> So in your case something like; >> >> nonZero <- (width(trimmedCoords)!=0) >> narrow(reads[nonZero], start=start(trimmedCoords)[nonZero], >> end=end(trimmedCoords)[nonZero]) >> >> Marcus >> >> >> On Sat, Mar 10, 2012 at 12:10 AM, Martin Morgan <mtmorgan@fhcrc.org>wrote: >> >>> On 03/08/2012 04:40 PM, wang peter wrote: >>> >>>> reads<- readFastq(fastqfile); >>>> seqs<- sread(reads); >>>> max.mismatchs<- mismatch_rate*1:nchar(**DNAString(PCR2rc)) >>>> trimmedCoords<- trimLRPatterns(Rpattern = PCR2rc, subject = seqs, >>>> max.Rmismatch= max.mismatchs, with.Rindels=T,ranges=T) >>>> >>>> end(trimmedCoords)[1:20] >>>>> >>>> [1] 22 18 20 33 14 22 22 20 22 22 22 15 20 37 19 13 20 22 0 34 >>>> >>>>> start(trimmedCoords)[1:20] >>>>> >>>> [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 >>>> >>>> there is a "0" in the end of trimmedCoords so i cannot get the trimmed >>>> sequences >>>> >>> >>> The sequence has been trimmed entirely >>> >>> > as.character(Views(DNAString("**AA"), IRanges(1, 1))) >>> [1] "A" >>> > as.character(Views(DNAString("**AA"), IRanges(1, 0))) >>> [1] "" >>> >>> Martin >>> >>> >>> >>>> trimmed3End<- narrow(reads, start=end(trimmedCoords), end=width(reads)) >>>> >>>> R version 2.14.1 (2011-12-22) >>>> Platform: x86_64-redhat-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=C LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] ShortRead_1.12.4 latticeExtra_0.6-19 RColorBrewer_1.0-5 >>>> [4] Rsamtools_1.6.3 lattice_0.20-0 Biostrings_2.22.0 >>>> [7] GenomicRanges_1.6.7 IRanges_1.12.6 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] Biobase_2.14.0 bitops_1.0-4.1 BSgenome_1.22.0 >>>> grid_2.14.1 >>>> [5] hwriter_1.3 RCurl_1.91-1 rtracklayer_1.14.4 >>>> tools_2.14.1 >>>> [9] XML_3.9-4 zlibbioc_1.0.0 >>>> >>>> >>> >>> -- >>> Computational Biology >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >>> >>> Location: M1-B861 >>> Telephone: 206 667-2793 >>> >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >> >> > [[alternative HTML version deleted]]
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