Hi Brian, I'm putting this on the mailing list since this might actually affect other users. Brian Herb wrote: > Herve- > > You perviously helped me with building the BSgenome package for the Rat, > and now i am helping my lab mate create a BSgenome package for the > rhesus monkey. We are running into an error when he reads in the gap files: > > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, > na.strings, : > scan() expected 'an integer', got 'fragment' > > we wonder if the issue is that the gap files are in a slightly different > format than what I am used to with the rat: > > Example Rat gap file: > > 585 chr1 1360 2576 2 N 1216 fragment yes > 585 chr1 5378 5428 4 N 50 fragment yes > 585 chr1 13845 13895 6 N 50 fragment yes > 585 chr1 23435 23485 8 N 50 fragment yes > 585 chr1 25955 26005 10 N 50 fragment yes > 585 chr1 33306 33356 12 N 50 fragment yes > 585 chr1 35384 40627 14 N 5243 fragment yes > 585 chr1 45904 46169 16 N 265 fragment yes > > Example rhesus monkey gap file: > > > chr1 17248 17350 2 N 102 fragment yes > chr1 26206 26619 4 N 413 fragment yes > chr1 27937 28130 6 N 193 fragment yes > chr1 47170 48593 8 N 1423 fragment yes > chr1 83907 85189 10 N 1282 fragment yes > chr1 95455 96505 12 N 1050 fragment yes > chr1 100303 100323 14 N 20 fragment yes > chr1 132263 132283 16 N 20 fragment yes > chr1 151325 152178 18 N 853 fragment yes Good catch! It seems that we can't indeed assume that UCSC is using a consistent schema for their 'gap' table. For Rat and any other organisms I've seen to far, the columns are the following: http://genome.ucsc.edu/cgi-bin/hgTables?db=rn4&hgta_group=map&hgta_tra ck=gap&hgta_table=gap&hgta_doSchema=describe+table+schema but for Rhesus, the 'bin' column is missing: http://genome.ucsc.edu/cgi-bin/hgTables?db=rheMac2&hgta_group=map&hgta _track=gap&hgta_table=gap&hgta_doSchema=describe+table+schema I've tried to accommodate this in read.gapMask(). This change will be available in IRanges >= 1.5.56 (devel) and IRanges >= 1.4.13 (release). Both packages should become available thru biocLite() in the next 24 hours. Please let me know if you encounter any further issue. Thanks for the report! H. > > we wonder if the missing column in the monkey gap file is throwing off > the forgeMasksFiles function, and if there is something that we can > stipulate in this function to change which column it is looking for. > > > > sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-unknown-linux-gnu > locale: > [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C > [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 > [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 > [7] LC_PAPER=en_US.iso885915 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] BSgenome_1.14.2 Biostrings_2.14.10 IRanges_1.4.9 > loaded via a namespace (and not attached): > [1] Biobase_2.6.0 > > Kind Regards, > Brian > > > -- > Brian Herb > Graduate Program in Biochemistry, Cellular and Molecular Biology > Johns Hopkins School of Medicine > Dr. Andrew Feinberg Laboratory > Rangos 580 > 855 N. Wolfe St. > Baltimore, MD 21205 > Phone:410-614-3479 > Fax: 410-614-9819 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319