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root/gclib/scripts/bltn
Revision: 24
Committed: Tue Jul 26 21:46:39 2011 UTC (8 years, 1 month ago) by gpertea
File size: 667 byte(s)
Log Message:
Line File contents
1 #!/bin/tcsh -f
2
3 if ($2'x' == 'x') then
4 echo "Usage: \n bltn 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 " x - to use tblastx instead of blastn"
8 echo " p - if qry is protein (tblastn)"
9 exit 1
10 endif
11
12 set fqry=$1
13 shift
14 set fdb=$1
15 shift
16 set qparams='-q=rna -t=dna'
17 if ($1 == 'x') then
18 set qparams='-q=dnax -t=dnax'
19 else
20 if ($1 == 'p') then
21 set qparams='-q=prot -t=dnax'
22 endif
23 endif
24
25 if (-f $fqry && -f $fdb) then
26 echo "# running: gblat $qparams -out=gff $fdb $fqry stdout"
27 gblat -noHead $qparams -out=gff $fdb $fqry stdout
28 else
29 echo "$fqry or $fdb not found!"
30 endif

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svn:executable *