[EMBOSS] Restrict- exclude range
bcitron at health.usf.edu
Tue Oct 12 12:23:49 EDT 2010
Your point about "not directly" inspired me to generate an alias in a .src file. If one keeps a list of favorite restriction enzymes in a file called lmbenz.dat (containing one restriction enzyme name per line) in a directory like ~/sequences, then the command:
re t.gbk 300 500
Will generate restrict output only showing enzymes that do not cut within the region 300 to 500 in the sequence named as the first parameter, t.gbk in this case.
alias re 'restrict -auto \!:1 re.tmp -enz=@~bcitron/sequences/lmbenz.dat -sb \!:2 -sen \!:3 -rformat2 simple; grep name re.tmp| sed s/"Enzyme_name: "//g > rel.tmp; grep -v -f rel.tmp ~bcitron/sequences/lmbenz.dat > rene.dat; restrict -auto \!:1 stdout -email@example.com'
There are probably better ways to accomplish this, and with intermediate files, one should be able to show the excluded enzymes and other enzyme sets. And there may be output options for restrict that don't require quite the grep and sed cleanup. Also, it should certainly be possible to adjust this for multiple exclusion ranges, etc.
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