Difference between revisions of "Run.pl"
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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. |
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| − | Usage: perl run.pl --in <input sequence file> --out_b <output blast file> --out_p <output psiblast file> --out_h <output hhblits file> [options] |
+ | Usage: perl run.pl --in <input sequence file> --out_b <output blast file> --out_p <output psiblast file> --out_h <output hhblits file> [options] <br> |
| − | --db_b <database BLAST/Psi-BLAST> default=big_80 |
+ | --db_b <database BLAST/Psi-BLAST> default=big_80 <br> |
| − | --db_h <database HHblits> default=uniprot20 |
+ | --db_h <database HHblits> default=uniprot20 <br> |
| − | --iter_p <number of iterations Psi-BLAST> default=2 (in this script) |
+ | --iter_p <number of iterations Psi-BLAST> default=2 (in this script) <br> |
| − | --iter_h <number of iterations HHblits,[1,8]> default=2 |
+ | --iter_h <number of iterations HHblits,[1,8]> default=2 <br> |
| − | --eval_p <E-Value cutoff for Psi-BLAST, [0,1]> default=0.002 |
+ | --eval_p <E-Value cutoff for Psi-BLAST, [0,1]> default=0.002 <br> |
| − | --eval_h <E-Value cutoff for HHblits, [0,1]> default=0.001 |
+ | --eval_h <E-Value cutoff for HHblits, [0,1]> default=0.001 <br> |
| − | --c <checkpoins Psi-BLAST file name> ckeckpoint PSSM file should be created to search in other iterations (in other database) |
+ | --c <checkpoins Psi-BLAST file name> ckeckpoint PSSM file should be created to search in other iterations (in other database) <br> |
| − | --r <checkpoins Psi-BLAST file name> ckeckpoint PSSM file to be reused 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) <br> |
| − | --h prints this usage |
+ | --h prints this usage <br> |
Revision as of 13:17, 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
