Re: Unix program wrapper problem
Re: Unix program wrapper problem
- Subject: Re: Unix program wrapper problem
- From: Sarven Sabunciyan <email@hidden>
- Date: Mon, 6 Feb 2006 00:06:26 -0500
Separating the arguments fixed the problem. i.e. instead of using
[blastArgs addObject:@"-p blastn"];
using
[blastArgs addObject:@"-p"];
[blastArgs addObject:@"blastn"];
makes everything work correctly.
Thank you all for all your help.
Regards
Sarven
On Feb 3, 2006, at 4:04 PM, email@hidden wrote:
Here is the problem. I have a set of unix database searching programs in the
directory:
/Blast/bin
So when I use the command 'cd /Blast/bin'
and then
'/Blast/bin/blastall -p blastn -d ecoli.nt -i test.txt -o out.txt'
The blastall program compares the contents of the file test.txt against the
ecoli.nt database and outputs the results in out.txt (which it
creates). There
are absolutely no problems. Note that test.txt and ecoli.nt are in
/Blast/bin as well that's why I switch to that directory.
I want to write a wrapper so that I can run the command from a mac
app. I am using the code example I found in Cocoa programming.
When I try to run the program (code is below) I get the following error:
[NULL_Caption] FATAL ERROR: blast: Unable to open input file test.txt
I try writing full path names for the database and the input file -
didn't work. Any ideas of what I am doing wrong. My code is
listed below.
[snip]
[blastArgs addObject:@"-p blastn"];
[blastArgs addObject:@"-d ecoli.nt"];
[blastArgs addObject:@"-i test.txt"];
[blastArgs addObject:@"-o testout.txt"];
Each of these should be two arguments. What you are doing would be
the equivalent of typing this on the command-line:
/Blast/bin/blastall "-p blastn" "-d ecoli.nt" "-i test.txt" "-o out.txt"
Remember that in shells, the space character is the argument
delimeter, so every time there is an (unquoted) space you are
starting a new argument.
Derrick
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