Description Usage Arguments Value Author(s) See Also Examples
Generate a QSLIMFinder command
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | QSLIMFinderCommand(file_list, i = 1,
slimpath = "../software/slimsuite/tools/",
blast = "../software/ncbi_blast_2.6.0/bin/",
iupred = "../software/iupred/iupred",
options = "dismask=T consmask=F cloudfix=F probcut=0.1",
LSF_cluster_par = "bsub -n 1 -q research-rh7 -M 100 -R \"rusage[mem=100]\"",
LSF_project_path = "/hps/nobackup/research/petsalaki/users/vitalii/vitalii/viral_project/",
analysis_type = c("qslimfinder", "slimfinder")[1])
mQSLIMFinderCommand(file_list, slimpath = "../software/slimsuite/tools/",
blast = "../software/ncbi_blast_2.6.0/bin/",
iupred = "../software/iupred/iupred",
options = "dismask=T consmask=F cloudfix=F probcut=0.5",
LSF_cluster_mode = F,
LSF_project_path = "/hps/nobackup/research/petsalaki/users/vitalii/vitalii/viral_project/",
LSF_cluster_par = "bsub -n 1 -q research-rh7 -M 200 -R \"rusage[mem=200]\"",
log_dir = "./SLIMFinder/log_dir/", write_log = T, recursive = F,
analysis_type = c("qslimfinder", "slimfinder")[1])
groupQSLIMFinderCommand(commands, InteractionSubsetFASTA_list,
sh_dir = "/sh_dir/",
LSF_project_path = "/hps/nobackup/research/petsalaki/users/vitalii/vitalii/viral_project/",
dataset_name = "SLIMFinder", N_seq = 200, write_log = T)
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file_list |
data.table containing path to files and directories for QSLIMFinder: fastafile, queryfile, outputdir, outputfile |
i |
integer, which set of files and directories to choose from |
slimpath |
relative path (from the project folder) to the directory containing qslimfinder.py or slimfinder.py |
blast |
relative path (from the project folder) to /bin/ folder in BLAST package |
iupred |
relative path (from the project folder) to iupred (compiled executable) |
options |
any options from QSLIMFinder |
LSF_cluster_par |
a string that will launch LSF job |
LSF_project_path |
absolute path on LSF cluster |
analysis_type |
character 1L, qslimfinder or slimfinder. slimfinder doesn't need query: identical datasets with the same query will be removed and query files not written) |
LSF_cluster_mode |
logical, if FALSE |
log_dir |
character, directory where to write log files (stout and sterr) |
write_log |
whether to save stout and sterr |
commands |
list returned by |
InteractionSubsetFASTA_list |
object of class InteractionSubsetFASTA_list containing: FASTA sequences for interacting proteins, molecular interaction data they correspond to. Each element of a list contains input for individual QSLIMFinder run. |
sh_dir |
directory within dataset directory (dataset_name) where to write batch command .sh files |
dataset_name |
character, name of the dataset, such as "SLIMFinder" or "SLIMFinder_Vidal" |
N_seq |
size of the batch. Groups QSLIMFinder jobs until the next job doesn't fit into N_seq, if jobs is larger than N_seq a single job will be written to a batch .sh file. |
LSF_project_path |
full path to the project where dataset directory (dataset_name) is located. |
write_log |
FALSE will not allow runQSLIMFinder to detect crashed jobs |
character vector (1L), bash command that will lauch QSLIMFinder locally or as a job on LSF cluster
list containing: 1. command to set up enviromental variable IUPred_PATH; 2. character vector of bash commands that will lauch QSLIMFinder as a job on LSF cluster; 3, 4, 5 - directories where LSF should write stout and sterr
QSLIMFinderCommand split into batches by N_seq sequences. List containing: 1. command to set up enviromental variable IUPred_PATH; 2. character vector of bash commands that will lauch $SHELL as a job on LSF cluster and run QSLIMFinder commands from batch file; 3, 4, 5 - directories where LSF should write stout and sterr
Vitalii Kleshchevnikov
listInteractionSubsetFASTA
, runQSLIMFinder
1 2 3 4 5 6 7 8 | all_commands = mQSLIMFinderCommand(file_list = forSLIMFinder_file_list,
slimpath = "../software/cluster/slimsuite/tools/qslimfinder.py",
blast = "../software/cluster/ncbi_blast_2.6.0/bin/",
iupred = "../software/cluster/iupred/iupred",
options = "dismask=T consmask=F cloudfix=T probcut=0.3 iuchdir=T",
LSF_cluster_mode = T,
LSF_project_path = "/hps/nobackup/research/petsalaki/users/vitalii/vitalii/viral_project/",
LSF_cluster_par = "bsub -n 1 -q research-rh7 -M 100 -R \"rusage[mem=100]\"")
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