An engineer on staff adds: Process substitution is just another way to read from a pipe, so if blat reads the file more than once, it will not work.
Perhaps if bash had implemented it as a temp file instead of as a pipe it would work. -Galt 6/8/2010 12:00 PM, Galt Barber: > > We don't use process substitution. > We know nothing about how it works. > You can read the BLAT source. > > I will send the author Jim Kent > a short note about your question. > > -Galt > > 6/8/2010 10:44 AM, Peng Yu: >> I try to use process substitution (basically,<(cmd) in bash). But it >> doesn't work for blat. See below for the comparsion between with >> process substitution and without. >> >> Could you please let me know why it is not working for blat? >> >> $ cat query.fasta >>> test_sequence >> cttgcaccggaaagtctgctccaga >> $ cat database.fasta >>> chr1 >> cttgcaccggaaagtctgctccaga >> $ make >> blat -t=dna -q=dna -minScore=25 -maxGap=0 \ >> database.fasta \ >> query.fasta \ >> query.psl >> Loaded 25 letters in 1 sequences >> Searched 25 bases in 1 sequences >> blat -t=dna -q=dna -minScore=25 -maxGap=0 \ >> <(cat database.fasta) \ >> <(cat query.fasta) \ >> query1.psl >> Loaded 0 letters in 0 sequences >> Searched 0 bases in 0 sequences >> $ cat query.psl >> psLayout version 3 >> >> match mis- rep. N's Q gap Q gap T gap T gap strand >> Q Q Q >> Q T T T T block blockSizes >> qStarts tStarts >> match match count bases count bases >> name >> size start end name size start end count >> --------------------------------------------------------------------------------------------------------------------------------------------------------------- >> 25 0 0 0 0 0 0 0 + >> test_sequence 25 0 25 chr1 25 0 25 1 >> 25, 0, 0, >> $ cat query1.psl >> psLayout version 3 >> >> match mis- rep. N's Q gap Q gap T gap T gap strand >> Q Q Q >> Q T T T T block blockSizes >> qStarts tStarts >> match match count bases count bases >> name >> size start end name size start end count >> --------------------------------------------------------------------------------------------------------------------------------------------------------------- >> >> > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
