Question: Problems running ps_scan.pl
0
gravatar for bzamith26
3.7 years ago by
bzamith2610
Brazil
bzamith2610 wrote:

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 (https://www.biostars.org/p/156140/).

 

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 thats 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

ps_scan prosite • 1.3k views
ADD COMMENTlink modified 3.7 years ago by Jean-Karim Heriche18k • written 3.7 years ago by bzamith2610
1
gravatar for Jean-Karim Heriche
3.7 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

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).

ADD COMMENTlink written 3.7 years ago by Jean-Karim Heriche18k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1035 users visited in the last hour