Difference between revisions of "Run.pl"
Kalemanovm (talk | contribs) (→run.pl) |
Kalemanovm (talk | contribs) |
||
Line 3: | Line 3: | ||
You can find the script run.pl here on biocluster: <code>/mnt/home/student/kalemanovm/master_practical/Assignment2_Alignments/scripts/task1</code>. The usage of the script with examples can also be found in the header of the file itself. |
You can find the script run.pl here on biocluster: <code>/mnt/home/student/kalemanovm/master_practical/Assignment2_Alignments/scripts/task1</code>. The usage of the script with examples can also be found in the header of the file itself. |
||
− | + | Usage: perl run.pl --in <input sequence file> --out_b <output blast file> --out_p <output psiblast file> --out_h <output hhblits file> [options] |
|
− | + | --db_b <database BLAST/Psi-BLAST> default=big_80 |
|
− | + | --db_h <database HHblits> default=uniprot20 |
|
− | + | --iter_p <number of iterations Psi-BLAST> default=2 (in this script) |
|
− | + | --iter_h <number of iterations HHblits,[1,8]> default=2 |
|
+ | --eval_p <E-Value cutoff for Psi-BLAST, [0,1]> default=0.002 |
||
− | --c <checkpoins file name. ckeckpoint PSSM file should be created to search in other iterations (in other database) <br> |
||
+ | --eval_h <E-Value cutoff for HHblits, [0,1]> default=0.001 |
||
− | --r <checkpoins file name. ckeckpoint PSSM file to be reused to search in other iterations (in other database) <br> |
||
+ | --c <checkpoins Psi-BLAST file name> ckeckpoint PSSM file should be created to search in other iterations (in other database) |
||
− | --h prints this usage |
||
+ | --r <checkpoins Psi-BLAST file name> ckeckpoint PSSM file to be reused to search in other iterations (in other database) |
||
+ | --h prints this usage |
Revision as of 13:16, 4 May 2013
Performs a BLAST/PSI-BLAST/HHblits run with custom parameters on biolab computers.
You can find the script run.pl here on biocluster: /mnt/home/student/kalemanovm/master_practical/Assignment2_Alignments/scripts/task1
. The usage of the script with examples can also be found in the header of the file itself.
Usage: perl run.pl --in <input sequence file> --out_b <output blast file> --out_p <output psiblast file> --out_h <output hhblits file> [options] --db_b <database BLAST/Psi-BLAST> default=big_80 --db_h <database HHblits> default=uniprot20 --iter_p <number of iterations Psi-BLAST> default=2 (in this script) --iter_h <number of iterations HHblits,[1,8]> default=2 --eval_p <E-Value cutoff for Psi-BLAST, [0,1]> default=0.002 --eval_h <E-Value cutoff for HHblits, [0,1]> default=0.001 --c <checkpoins Psi-BLAST file name> ckeckpoint PSSM file should be created to search in other iterations (in other database) --r <checkpoins Psi-BLAST file name> ckeckpoint PSSM file to be reused to search in other iterations (in other database) --h prints this usage