Malcolm, you're right that the wigToBigWig program will take input from standard in. The bedGraphToBigWig program will not, as it does a few passes over the data.
On Tue, Mar 22, 2011 at 12:52 PM, Cook, Malcolm <[email protected]> wrote: > word wrap is decidedly not my friend > > I hope this is a better formatted counter-example: > > curl ftp://hgdownload.cse.ucsc.edu/goldenPath/dm3/phastCons15way/chr4.pp.gz | > \ > gunzip -c | \ > wigToBigWig -clip stdin <(fetchChromSizes dm3) stdout > \ > phastCons15way_chr4.bw > > bigWigInfo phastCons15way_chr4.bw > > > ~Malcolm > > >> -----Original Message----- >> From: [email protected] >> [mailto:[email protected]] On Behalf Of Cook, Malcolm >> Sent: Tuesday, March 22, 2011 2:22 PM >> To: 'Brooke Rhead'; 'John Herbert' >> Cc: '[email protected]' >> Subject: Re: [Genome] bedGraphToBigWig; reading in from STDIN >> >> Brooke, >> >> Hmmm.... my mileage varies.... >> >> I have found that at least wigToBigWig can stream stdin, as >> the following example should prove: >> >> > curl >> > >> ftp://hgdownload.cse.ucsc.edu/goldenPath/dm3/phastCons15way/ch >> r4.pp.gz >> > | gunzip -c | wigToBigWig -clip stdin <(fetchChromSizes >> dm3) stdout > >> > phastCons15way_chr4.bw bigWigInfo phastCons15way_chr4.bw >> >> ?? >> >> Malcolm Cook >> Stowers Institute for Medical Research - Bioinformatics >> Kansas City, Missouri USA >> >> >> >> > -----Original Message----- >> > From: [email protected] >> > [mailto:[email protected]] On Behalf Of Brooke Rhead >> > Sent: Tuesday, March 22, 2011 1:22 PM >> > To: John Herbert >> > Cc: [email protected] >> > Subject: Re: [Genome] bedGraphToBigWig; reading in from STDIN >> > >> > Hi John, >> > >> > It is not possible for the *ToBig* utilities to use STDIN >> and STDOUT, >> > as they need to do two passes over the file. >> > >> > If you have any further questions, please feel free to contact us >> > again at [email protected]. >> > >> > -- >> > Brooke Rhead >> > UCSC Genome Bioinformatics Group >> > >> > >> > John Herbert wrote on 3/22/11 7:53 AM: >> > > Dear UCSC, >> > > Please can you tell me if it is possible to run the binary >> > bedGraphToBigWig feeding in from STDIN? >> > > >> > > I would like to do something like; ./peaks_to_bedgraph.pl file | >> > bedGraphToBigWig stdin dm3_sizes output.bigwig (I also make the >> > assumption that sort command can write to STDOUT). >> > > >> > > Any help appreciated and sorry if I missed this option. >> > > Kind regards, >> > > >> > > John. >> > > _______________________________________________ >> > > Genome maillist - [email protected] >> > > https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ >> > Genome maillist - [email protected] >> > https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
