is matchPattern faster?
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wang peter ★ 2.0k
@wang-peter-4647
Last seen 8.4 years ago
i have some reads from illumina sequencer there are some "N" in the reads i want to find the last "N" in the first 6 bp of the sequence so do you think matchPattern is faster ? or other low-level match methods? reads <- readFastq(fastqfile) seqs <- sread(reads); matchPattern("N", seqs) -- 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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@harris-a-jaffee-3972
Last seen 8.3 years ago
United States
Perhaps something along the lines r = reverse(narrow(seqs, 1, 6)) answer = 7 - which.isMatchingAt("N", r, at=1:6) On Jan 19, 2012, at 5:26 PM, wang peter wrote: > i have some reads from illumina sequencer > there are some "N" in the reads > i want to find the last "N" in the first 6 bp of the sequence > so do you think matchPattern is faster ? or other low-level match methods? > > reads <- readFastq(fastqfile) > seqs <- sread(reads); > matchPattern("N", seqs) > > > > -- > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Or maybe n = narrow(seqs, 1, 6) answer = 6 - nchar(sub(".*N", "", n)) On Jan 19, 2012, at 6:01 PM, Harris A. Jaffee wrote: > Perhaps something along the lines > > r = reverse(narrow(seqs, 1, 6)) > answer = 7 - which.isMatchingAt("N", r, at=1:6) > > On Jan 19, 2012, at 5:26 PM, wang peter wrote: >> i have some reads from illumina sequencer >> there are some "N" in the reads >> i want to find the last "N" in the first 6 bp of the sequence >> so do you think matchPattern is faster ? or other low-level match methods? >> >> reads <- readFastq(fastqfile) >> seqs <- sread(reads); >> matchPattern("N", seqs) >> >> >> >> -- >> 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Sorry, I'll get it eventually. answer = which.isMatchingAt("N", seqs, at=6:1, follow.index=TRUE) Let me know if anything beats it. On Jan 19, 2012, at 6:15 PM, Harris A. Jaffee wrote: > Or maybe > > n = narrow(seqs, 1, 6) > answer = 6 - nchar(sub(".*N", "", n)) > > On Jan 19, 2012, at 6:01 PM, Harris A. Jaffee wrote: >> Perhaps something along the lines >> >> r = reverse(narrow(seqs, 1, 6)) >> answer = 7 - which.isMatchingAt("N", r, at=1:6) >> >> On Jan 19, 2012, at 5:26 PM, wang peter wrote: >>> i have some reads from illumina sequencer >>> there are some "N" in the reads >>> i want to find the last "N" in the first 6 bp of the sequence >>> so do you think matchPattern is faster ? or other low-level match >>> methods? >>> >>> reads <- readFastq(fastqfile) >>> seqs <- sread(reads); >>> matchPattern("N", seqs) >>> >>> >>> >>> -- >>> 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 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/ >>> gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/ >> gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor
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