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
