Problems running ps_scan.pl

Question

[bzamith26]

Dear all,

I was wondering if you could help me to solve a problem.

I've already asked a question about ps_scan, but it was the wrong question (I asked about pfscan when I needed to ask about ps_scan). I am sorry about that :( However, I appreciate all the answers I've received (Problems with entering a sequence on Pfscan (Prosite)).

But what I really need to do is scan a sequence of proteins against prosite database. I have already done that on the online tool and it worked pretty well.

So, I am using now the command:

perl ps_scan.pl -s seq.fasta -o fasta

And that's what I get:

open2: exec of pfscan -flxz -v - prosite.dat L=-1 failed at ps_scan.pl line 1900.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
ERROR: 'pfscan' execution failed.
            Check pfscan is in your PATH
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

Here are the images where you can see the terminal and the folder with everything I've downloaded:

• http://i.imgur.com/eZPGmxd.png
• http://i.imgur.com/7K6JR6X.png

I read some suggestions here on biostars, like this one:

In the README there is a note covering this:

You may need to edit the ps_scan.pl to provide absolute paths to the directory where you have installed the pfscan and psa2msa executables, unless you have stored them in a directory in your PATH.

And looking in the code for ps_scan.pl there is this section:

# change this to the absolute path to the programs,
# unless they are located in a directory in your PATH
# or use option --pfscan and/or --psa2msa to give the full path.
my $PFSCAN  = 'pfscan';
my $PSA2MSA = 'psa2msa';

I couldn't really understand that. I am a freshman on Linux and Bioinformatics.

Thanks in advance

Best Regards,
Bruna

Answer 1

[Jean-Karim Heriche]

Find where your programs pfscan and psa2ma are (if you didn't install them yourself, ask the person who did). Assuming they are in /usr/local/bin, change

my $PFSCAN = 'pfscan';

to

my $PFSCAN = '/usr/local/bin/pfscan';

Before going much further in the field, I suggest you get some basic knowledge about the Linux command line terminal. There are plenty of books on the subject and tutorials online (e.g. here).