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root/gclib/scripts/run_pexonerate
Revision: 24
Committed: Tue Jul 26 21:46:39 2011 UTC (8 years, 1 month ago) by gpertea
File size: 535 byte(s)
Log Message:
Line File contents
1 #!/bin/tcsh -f
2 if ( $2'x' == 'x' ) then
3 echo "Usage: \nrun_pexonerate <prot_fasta> <genomic_seq_fasta> [<output_gff>]"
4 exit
5 endif
6
7 set excmd='exonerate -V 0 --model p2g --percent 20 -n 11 --showalignment no --showtargetgff yes --showvulgar no'
8 set excmd="$excmd --maxintron 450000 --seedrepeat 2 --ryo "'%ti\t%qi\tmap_end\t%r\t%ql|%qab-%qae\t%ps\t%g\t%qd\n'
9 set excmd="$excmd --geneseed 60 -x 50 --proteinwordlen 4 --saturatethreshold 80 $1 $2"
10
11 if ( $3'x' == 'x' ) then
12 $excmd
13 else
14 $excmd | fltexonerate -c70 -p70 > $3
15 endif

Properties

Name Value
svn:executable *