UNIX for Dummies Questions & Answers

Hello all-

First post, so just to forewarn you: I know enough about Perl and the Terminal to get myself into trouble, not quite enough to always get out.

I'd like to know if it is possible to, from the command prompt, use a wild-card to declare the names of files for input and then use the value of the wild card in the same line to declare the name for the output. I'm using the BLAST package to search through genes, so what I'd like to have is:

% blastall -p blastn -i *.dna -o (some-variable).output

The -p calls the blastn part of the package, the -i declares the input to be all the genes in the directory and the -o declares the output. I'd like it if a geneA.dna file, for instance, produced an output file called geneA.output.

It strikes me as one of those glaringly obvious things I've overlooked at some point, but I have no idea what could be put in the (some-variable) portion of the command. Gory details: using the public BLAST package (so I can't edit anything within there easily to... at all), executing on a Mac OS X Terminal session. If you need any other details, please let me know.

Very do-able but not as easily as you'd hope:

Code:

for file in *.dna; do blastall -p blastn -i $file -o ${file}.output

Will produce a bunch of files *.dna.output
To get *.output:

Code:

for file in *.dna; do blastall -p blastn -i $file -o `echo $file | sed 's/dna$//'`.output

Incidentally, windows actually lets you do something like this:

Code:

blastall -p blastn -i *.dna -o *.output

But only for certain commands - it seems to depend on how you hold your mouth when you do it.