Hi Kyle, The "o" and "t" values in the url of a details page refer to the actual base location of the SNP. These values be derived from the snp130 table using the rs number (snp130.name) - which is also "i" in the url.
portion of url with pointer to table snp130 for your example: rs72477211 o=10259&t=10260&g=snp130&i=rs72477211 o = snp130.chromStart +1 (0-based coordinates -> 1-based) t = snp130.chromEnd i = snp130.name -- details page from hg18 for your example: rs72477211 -- dbSNP build 130 rs72477211 dbSNP: rs72477211 Position: chr1:10260-10260 Band: 1p36.33 Genomic Size: 1 View DNA for this feature Strand: + Observed: A/G Reference allele: C Class: single Validation: unknown Function: unknown Molecule Type: genomic Weight: 1 ------------------------------------------- I hope this information is helpful. Please feel free to contact the help mailing list again if you require further assistance. Best regards, Jen UCSC Genome Browser Support http://genome.ucsc.edu/contacts.html [email protected] [email protected] On 6/10/10 1:50 PM, Kyle Tretina wrote: > Hello, > > For this particular rs72477211, we see the file offset in snp130Seq is > 17524345321. On the web page, we see o=10259&t=10260. Is there a reasonable > way, given the rsnumber, obtain the 'o' and 't' values? > > > > > Kyle Tretina > > On Tue, Jun 8, 2010 at 12:36 PM, Angie Hinrichs<[email protected]> wrote: > >> P.S. actually I would like to change "long offset = 0;" to "off_t offset = >> 0;". getSnpSeqFileOffset already returns off_t so I believe that should >> work fine on 32 bits with -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE . >> >> Thanks again, >> >> Angie >> >> >> ----- "John Hayward"<[email protected]> wrote: >>> From: "John Hayward"<[email protected]> >>> To: "John Hayward"<[email protected]>, "Angie Hinrichs"< >> [email protected]>, "Kyle Tretina"<[email protected]> >>> Cc: "UCSC"<[email protected]> >>> Sent: Tuesday, June 8, 2010 8:51:03 AM GMT -08:00 US/Canada Pacific >> >>> Subject: RE: [Genome] Fwd: Fwd: Problem with Mirror >>> >>> >>> >>> Hi Angie, >>> We were able to get our queries to work after making changes to >> getSnpSeqFileOffset >>> function in hgc.c. It appears that the original code does not work in a >> 32 bit environment. Here are the changes we needed to do to have it work in >> our setting: >>> 1) Line 23137 change declaration of offset >>> === was >>> long offset = 0; >>> === to >>> long long offset = 0; >>> >>> 2) Line 23135 change call of conversion of returned sql offset: >>> ==== was >>> offset = sqlUnsignedLong(row[0]) >>> === to >>> offset = sqlLongLong(row[0]) >>> >>> I don't know if there are other 32/64 issues but it may be helpful to >> others working in a 32 bit environment to have these adjustments made in the >> code. >>> >>> Thanks for your help in locating this problem. >>> >>> johnh... >>> >>> >> ------------------------------ >>> *From:* John Hayward >>> *Sent:* Tuesday, June 08, 2010 9:51 AM >>> *To:* Angie Hinrichs; Kyle Tretina >>> *Cc:* UCSC >>> *Subject:* RE: [Genome] Fwd: Fwd: Problem with Mirror >>> >>> >> > >>> The problem seems to be a 64/32 bit issue. >>> I rebuilt the binaries and observed the flags for building (here is a >> snippet) >>> .... >>> gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type >> -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE >> -DMACHTYPE_i486 -Wall -Werror -Wformat -Wimplicit -Wreturn-type >> -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc >> -I../../../../../inc -o hgLoadWiggle.o -c hgLoadWiggle.c >>> .... >>> >>> The error on the web page we see is: >>> ===== >>> Expected FASTA header, got this line: >>> ATAATACATT TTAATTTTCT AGAAAGTAAT GGTATGAAGT TCCAACTTTT TTTAAAAAAG >> ACTTTTTTTC >>> at offset 344476137 in file /gbdb/hg18/snp/snp130.fa >>> ====== >>> The offset you are seeing from the database is 17524345321 >>> >>> Here is a bc script: >>> ===== >>> bc 1.06.94 >>> Copyright 1991-1994, 1997, 1998, 2000, 2004, 2006 Free Software >> Foundation, Inc. >>> This is free software with ABSOLUTELY NO WARRANTY. >>> For details type `warranty'. >>> obase=16 >>> 15 >>> F >>> 344476137 // this is the offset reported in the error >>> 148849E9 >>> 17524345321 // this is the offset according to the database >>> 4148849E9 // if you truncate this value to 32 bits (last 8 hex digits) >> then you get the value >>> // above >>> ====== >>> This shows that the offset in the database is more than 32 bits and when >> truncated to 32 bits is the same value reported in the error message. >>> >>> The operating system is: >>> Linux ubuntu 2.6.31-302-ec2 #7-Ubuntu SMP Tue Oct 13 19:06:04 UTC 2009 >> i686 GNU/Linux >>> Ubuntu 10.04 (lucid) >>> >>> Now we need to find out where the offset is being truncated - it seems >> that the flags for file offsets are in place but I wonder if there are some >> other 32 bit issues in the source. >>> >>> I recall when originally building there were some warnings which required >> some changes to compile. I think the next step is to repeat those steps and >> make sure there are no 32/64 bit issues. >>> >>> johnh... >>> >>> >> ------------------------------ >>> *From:* Angie Hinrichs [[email protected]] >>> *Sent:* Monday, June 07, 2010 5:26 PM >>> *To:* Kyle Tretina >>> *Cc:* UCSC; John Hayward >>> *Subject:* Re: [Genome] Fwd: Fwd: Problem with Mirror >>> >>> >> > Hi Kyle, >>> >>> I think I know what it is now: snp130.fa is an extremely large file, and >> either your operating system can't handle its size or perhaps the flags >> "-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE" were omitted from the build? >> (our makefiles all include kent/src/inc/common.mk, which defines the >> variable HG_DEFS to include those, and our compile rule uses $HG_DEFS) >>> >>> snp130.fa is a whopping 18,668,682,162 bytes. (18GB or 17GiB depending >> on how you count) If your filesystem can handle only 32-bit file offsets >> (or even 36), that is just too big. >>> >>> rs72477211's offset ("select file_offset from snp130Seq where acc = >> 'rs72477211'") is 17524345321, which is (16 * 1024 * 1024 * 1024) + >> 344476137, >> and 344476137 is the file offset that you see in the error message because >> the top bit of the offset is lost. >>> >>> What operating system and compiler are you using? >>> >>> Angie >>> >>> >>> ----- "Kyle Tretina"<[email protected]> wrote: >>>> From: "Kyle Tretina"<[email protected]> >>>> To: "Angie Hinrichs"<[email protected]>, "UCSC"<[email protected]>, >> "John Hayward"<[email protected]> >>>> Sent: Sunday, June 6, 2010 10:59:57 AM GMT -08:00 US/Canada Pacific >>>> Subject: Re: [Genome] Fwd: Fwd: Problem with Mirror >>>> >>>> Hello, >>>> >>>> >> Note: this was in database hg19 using the command: select settings from >> trackDb where tableName = "snp130"; >> ======================================================================= >> >>>> >> >> +--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ >> | settings >> >> >> >> >> >> | >> >> +--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ >> | chimpDb panTro2 >> chimpOrangMacOrthoTable snp130OrthoPt2Pa2Rm2 >> codingAnnoLabel_snp130CodingDbSnp dbSNP >> codingAnnotations snp130CodingDbSnp, >> defaultGeneTracks knownGene >> group varRep >> hapmapPhase III >> longLabel Simple Nucleotide Polymorphisms (dbSNP build 130) >> macaqueDb rheMac2 >> maxWindowToDraw 10000000 >> orangDb ponAbe2 >> priority 100.094 >> shortLabel SNPs (130) >> snpSeqFile /gbdb/hg18/snp/snp130.fa >> track snp130 >> type bed 6 + >> url http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ >> urlLabel dbSNP: >> visibility dense >> | >> >> +--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ >> 1 row in set (0.07 sec) >> >>>> >> >>>> >> ======================================================================= >> (This is the error message for rs72477211) >> >>>> >> *Error(s):* >> >> - Expected FASTA header, got this line: >> > > ATAATACATT TTAATTTTCT AGAAAGTAAT GGTATGAAGT TCCAACTTTT TTTAAAAAAG >> ACTTTTTTTC >> > > at offset 344476137 in file /gbdb/hg18/snp/snp130.fa >> >> ======================================================================= >> >>>> >> So rs242 does work. When I enter it into my mirror, I am getting the same >> output as your website. I was shocked when I saw it, because this was the >> first one I had entered that did not return an error message. >> >>>> >> >>>> >> Kyle Tretina >> Wheaton College >> >>>> >> >>>> >> >>>> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
