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
---------------------------------------------------------------------------------------------------------------------------------------------------------------
--
Regards,
Peng
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