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Torst · 08-10-2012, 06:03 PM

It's been that way since the batch mode was implemented for the old BLAST suite (via the "fastacmd" command). I can see your point about batch vs cmdline differences in capability.

It's not that limiting, as you can still do one at a time on the command line. So if you are able to create the 3 column batch file in "A B C" format, then you similarly should be able to create a batch file in "-entry A -range B -strand C" format and use a shell command to apply it:

% (for LINE in batch.txt ; do blastdbcmd -db mydb $LINE ; done) > output.fasta

Problem solved.

08-10-2012, 06:03 PM	#4
Torst Senior Member Location: The University of Melbourne, AUSTRALIA Join Date: Apr 2008 Posts: 275	It's been that way since the batch mode was implemented for the old BLAST suite (via the "fastacmd" command). I can see your point about batch vs cmdline differences in capability. It's not that limiting, as you can still do one at a time on the command line. So if you are able to create the 3 column batch file in "A B C" format, then you similarly should be able to create a batch file in "-entry A -range B -strand C" format and use a shell command to apply it: % (for LINE in batch.txt ; do blastdbcmd -db mydb $LINE ; done) > output.fasta Problem solved.