standalone ribopicker

[jdew...@apu.edu]

Hi. I am extremely inexperienced with programming, but I decided to give the standalone version a shot.

I tried putting in the following command:
perl ribopicker.pl -f {my file} -dbs rrnadb

And came up with the following error: cannot find all database files for database "rrnadb" in dir "db/"

So I downloaded several files from http://edwards.sdsu.edu/ribopicker/rrnadb/: humanrrna201220220.tar.gz and the taxon file, ncbibact20120227.tar.gz and taxon, rrnadb_2011-20-16.tag.gz and rrnadb_2012-02-17.tar.gz.
I put all these in the db file.

Then I used the following the command mentioned previously and I got output files, however, they're very large and I don't know how to open them.

I have 3 questions:
How do I open the files?
How do I extract sequence only?
Is it possible to use a different database? I would like to use humanrrna but I don't know what -dbs code to use.

[jdew...@apu.edu]

For question 3, when I tried
perl ribopicker.pl -f {my file} -dbs humanrrna
I got, database "humanrrna" does not exist in config file.

Is that riboPickerConfig.pm? How do I put "humanrrna" into the config file?

[Robert Schmieder]

You will need to add the humanrrna database to the config file under DBS in the riboPickerConfig.pm file similar to the following example, where humanrrna is the name that you call in your command and humanrrna_db is the name of the database file (without file extension):

humanrrna => { name => 'Human rRNA', db => 'humanrrna_db' },