[Bioc-sig-seq] Applying grep to a large number of tags. (looking for speed)

[Ivan Gregoretti]

Hello Patrick,

The idea of vcountPattern is good but it does not quite work for two reasons

1) mySeq is ~40kb. That is quite big and vcountPattern() throws the error

> vcountPattern(mySeq, sread(A))
Error in .valid.algos(pattern, max.mismatch, min.mismatch, with.indels,  :
  patterns with more than 20000 letters are not supported

2) vcountPattern is designed to find a motif (small) contained in a
genome (large), like this
vcountPattern("GCCACCAGGGGGCGC", Mmusculus)

In my case, I have millions of motifs (the 36 bp tags) that I have to
find if they are contained in my single ~40kb. Its like a reverse
scenario. So, if I try reversing the arguments, I also get an error:

> vcountPattern(sread(A), mySeq)
Error in normargPattern(pattern, subject) :
  'pattern' must be a single string or an XString object

Any more suggestions?

Thank you,

Ivan

> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-03-25 r51410)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=C
LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] annotate_1.27.1      AnnotationDbi_1.11.4 Biobase_2.9.0
ShortRead_1.7.9
[5] Rsamtools_1.1.8      lattice_0.18-8       Biostrings_2.17.24
GenomicRanges_1.1.17
[9] IRanges_1.7.12

loaded via a namespace (and not attached):
[1] DBI_0.2-5     grid_2.12.0   hwriter_1.2   RSQLite_0.9-1 xtable_1.5-6
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