running external command in DOS

[perldoubt]

Hi,

Please help me.

I am tryinhg to run an external command on DOS using perl script.

Backtics do not work.

General syntax of the command is:


bl2seq -p programname -i firstfilename -j secondfilename -o

<outputfilenanme>

which in my program is :

C:\\xxx\\xxx\\xxx\\bl2seq\\bin\\bl2seq -p blastp -i C:\\xxx\\xxx\\xxx\\xx\\FH1 -j C:\\xxx\\xxx\\xxx\\xxx\\FH2 -o C:\\xxx\\xxx\\xxx\\xxx\\FH1.txt");

I am trying to call this using system();

Please help me.

Thanks,
perldoubt

 

[learingperl01]

Have you tried using quotes?

system("Command to run");

or you could save the command to a variable and then call the variable in the system command

command = "Command that you would like to run here";
print $command; # Make sure output looks correct when printed
system($command);

 

[perldoubt]

No man,
Its not working.
look at this..

this command at DOS works well.

bl2seq -p blastp
-i gi_57652444_r3.faa
-j gi_57652446_r2.faa
-o pp.txt
but when I write a script:
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
#!/usrlocal/bin/perl

$command = "bl2seq -p bl
astp -i gi_57652444_r3.faa -j gi_57652446_r2.faa -o pp.txt";
print $command."\n";
system($command);

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
bl2seq -p bl
astp -i gi_57652444_r3.faa -j gi_57652446_r2.faa -o pp.txt
[NULL_Caption] ERROR: Arguments must start with '-' (the offending argument #3 was: 'astp')

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Any suggestions?

 

[rharsh]

$command = "bl2seq  -p [red][b]bl
astp[/b][/red] -i gi_57652444_r3.faa    -j gi_57652446_r2.faa  -o pp.txt";

Is the section in red really broken up with a new line? I suspect that's not helping anything.

 

[travs69]

i suspect that rharsh is right because the error mentions starting with astp not blastp.

Also in your original code.. if you surroung everything with a single quote you don't have to use double black slashes. You also can just use forward slashes as dos/windows won't care. You should still use single quotes though. Unless there's a variable in those double quotes somewhere your just having perl do more work than necessary.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Travis - Those who say it cannot be done are usually interrupted by someone else doing it; Give the wrong symptoms, get the wrong solutions;

 

[goBoating]

the 'system' function expects to get your command and it's arguments in a list. I think passing all the arguments as pieces of a STRING will cause the function to barf.

Sorry, but, I don't have time to play with it to put an example together.

See c:\>perldoc -f system



'hope this helps

If you are new to Tek-Tips, please use descriptive titles, check the FAQs, and beware the evil typo.

 

[stevexff]

Here's an example. It's not tested, of course, as I dont have bl2seq on my system...

use strict;
use warnings;

my $file1 = "gi_57652444_r3.faa";
my $file2 = "gi_57652446_r2.faa";
my $outfile = "pp.txt";

system('bl2seq -p blastp -i', $file1, '-j', $file2, '-o', $outfile);

Steve

[small]"Every program can be reduced by one instruction, and every program has at least one bug. Therefore, any program can be reduced to one instruction which doesn't work." (Object:erlDesignPatterns)[/small]

 

[perldoubt]

Thanks Steve,That was perfect.

storing assigning filenames to a string var is an excellent idea.

IT's working now.
Thanks a ton.

Aparna

 

[KevinADC]

You also can just use forward slashes as dos/windows won't care.

DOS does care. The forward slash is an option switch in DOS, not a directory path, like it is in Windows.

------------------------------------------
- Kevin, perl coder unexceptional!

 

[perldoubt]

Thats right.

I used \\ to define path.
/\did'nt work.

 

[travs69]

DOH!!
Thanks Kevin

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Travis - Those who say it cannot be done are usually interrupted by someone else doing it; Give the wrong symptoms, get the wrong solutions;

 

[dave82]

Try to escape "-" with "\"

=> "\-option" when specifying one option.

Hope it helps

dave82

 

[smokinace]

How many sequences are you comparing?
I used the same program. bl2seq is fine for maybe a couple of sequences. If you have a ton of sequences it's probably a better idea to use blastall. instead of taking 60 days to do a billion comparisons, blastall did it in 5 hours.