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root/gclib/scripts/bln
Revision: 24
Committed: Tue Jul 26 21:46:39 2011 UTC (8 years, 1 month ago) by gpertea
File size: 735 byte(s)
Log Message:
Line File contents
1 #!/bin/tcsh -f
2
3 if ($2'x' == 'x') then
4 echo "Usage: \n bln qryseq(s).fasta dbseq.fasta [x|p]"
5 echo "dbseq.fasta must be a nucleotide sequence."
6 echo "The 3rd parameter can be:"
7 echo " t - use tblastx instead of blastn"
8 echo " p - qry is protein (tblastn)"
9 echo " x - qry is dna, db is protein (blastx)"
10 exit 1
11 endif
12
13 set fqry=$1
14 shift
15 set fdb=$1
16 shift
17 set prog=blastn
18 set fmtopt='-n'
19 if ($1 == 't') set prog=tblastx
20 if ($1 == 'p') set prog=tblastn
21 if ($1 == 'x') then
22 set prog=blastx
23 set fmtopt='-p'
24 endif
25
26 if (-f $fqry && -f $fdb) then
27 xdformat $fmtopt $fdb
28 echo "RUNNING: $prog $fdb $fqry E=0.01 -topcomboN 1 -cpus 1"
29 $prog $fdb $fqry E=0.01 -topcomboN 1 -cpus 1
30 else
31 echo "$fqry or $fdb not found!"
32 endif

Properties

Name Value
svn:executable *