Small correction: I used this file to locate the source (is on the web only, not in the kent source) http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/sources
To do a regular search in the source, use a "find" at the top of the kent source, for example: $ find ./ -type f | grep -i mafspeciessubset Jennifer On 3/25/10 9:47 AM, Jennifer Jackson wrote: > Hi Shan, > > This was a bit tricky to find! > > ~kent/src/hg/ratStuff/mafSpeciesSubset/ > > I used this file to locate the source: > ~kent/src/sources > > Thanks, > Jen > > On 3/24/10 10:06 PM, 董珊 wrote: >> >> >> ---------- 已转发邮件 ---------- >> 发件人： *董珊* <[email protected] >> <mailto:[email protected]>> >> 日期： 2010年3月24日 下午3:03 >> 主题： Re: [Genome] Create multiple alignment of 12 Drosophila species >> genomes >> 收件人： Jennifer Jackson <[email protected] <mailto:[email protected]>> >> >> >> Hello Jennifer, >> >> There is a problem when I get the mafSpeciesSubset program. >> I have already follow the guide "Source tree compilation on >> Debian/Ubuntu" and the guide in >> _http://genome.ucsc.edu/admin/jk-install.html__._ >> But there is no "mafSpeciesSubset" in the kent/src/*. >> I don't know why. >> >> >> Thank you very much in advance! >> >> Shan >> >> >> 2010/3/23 Jennifer Jackson <[email protected] <mailto:[email protected]>> >> >> Hello, >> >> The utility mafFilter is the best choice: use option -speciesFilter. >> You do not need to set up the entire code tree or a mirror to use >> the utilities in the kent source tree. >> >> http://genomewiki.ucsc.edu/index.php/The_source_tree >> http://hgdownload.cse.ucsc.edu/downloads.html -> Source >> >> mafFilter - Filter out maf files. Output goes to standard out >> usage: >> mafFilter file(s).maf >> options: >> -tolerate - Just ignore bad input rather than aborting. >> -minCol=N - Filter out blocks with fewer than N columns (default 1) >> -minRow=N - Filter out blocks with fewer than N rows (default 2) >> -factor - Filter out scores below -minFactor * (ncol**2) * nrow >> -minFactor=N - Factor to use with -minFactor (default 5) >> -minScore=N - Minimum allowed score (alternative to -minFactor) >> -reject=filename - Save rejected blocks in filename >> -needComp=species - all alignments must have species as one of the >> component >> -overlap - Reject overlapping blocks in reference (assumes ordered >> blocks) >> -componentFilter=filename - Filter out blocks without a component >> listed in filename >> *-speciesFilter=filename* - Filter out blocks without a species >> listed in filename >> >> Hopefully this helps, >> Jennifer >> >> --------------------------------- >> Jennifer Jackson >> UCSC Genome Informatics Group >> http://genome.ucsc.edu/ >> >> >> On 3/22/10 1:42 AM, 董珊 wrote: >> >> Dear Genome list, >> >> I want to ask a question about creat a multiple alignment from >> pair-wise >> alignments from UCSC Genome Blowser. >> The whole genome multiple alignment I need is from 12 Drosophila >> species, >> but the multiple alignment data on UCSC Genome Blowser contain 3 >> excess >> species (A. gambiae, A. mellifera and T. castaneum). >> >> I know there is a complex method to use multiz/TBA to get >> multiple alignment >> from pair-wise alignments. >> However, these pair-wise alignments must in MAF format. >> But it seems difficult to get the format convert tool on Kent >> source. >> Do you know other method to remove the 3 excess species from the >> multiple >> alignment from UCSC Genome Blowser? >> >> Thank you very much in advance! >> >> Best regards! >> Shan >> _______________________________________________ >> Genome maillist - [email protected] >> <mailto:[email protected]> >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> >> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
