PPInetwork2SLIMFinder: Find linear motifs (QSLIMFinder or SLIMFinder) in the protein...

In vitkl/SLIMFinderR: Short Linear Motif Search Using QSLIMFinder, Protein Interaction Network and Binding Domain Inference

Description

Find linear motifs (QSLIMFinder or SLIMFinder) in the protein interaction network

Usage

PPInetwork2SLIMFinder(dataset_name = "SLIMFinder",
  interaction_main_set = all_human_interaction,
  interaction_query_set = all_viral_interaction,
  analysis_type = "qslimfinder",
  options = "dismask=T consmask=F cloudfix=T probcut=0.3 minwild=0 maxwild=2 slimlen=5 alphahelix=F maxseq=1500 savespace=1 iuchdir=T",
  domain_res_file = "./processed_data_files/what_we_find_VS_ELM_clust20171019.RData",
  domain_results_obj = "res_count", center_domains = F,
  filter_by_domain = F,
  fasta_path = "./data_files/all_human_viral_proteins.fasta",
  main_set_only = F, domain_pvalue_cutoff = 1,
  SLIMFinder_dir = paste0("./", dataset_name, "/"),
  LSF_project_path = "/hps/nobackup/research/petsalaki/users/vitalii/vitalii/viral_project/",
  software_path = "../software/cluster/", length_set1_min = 2,
  length_set2_min = 1, write_log = T, N_seq = 200,
  seed_list = NULL, query_list = NULL, memory_start = 350,
  memory_step = 100, compare_motifs = T, Njobs_limit = 490,
  CompariMotif3_dburl = "http://elm.eu.org/elms/elms_index.tsv",
  CompariMotif3_dbpath = "./data_files/",
  non_query_domain_res_file = "../viral_project/processed_data_files/predict_domain_human_clust20180819.RData",
  non_query_domain_results_obj = NULL, non_query_domains_N = 0,
  non_query_set_only = c(main_set_only), query_domains_only = T)

Arguments

dataset_name	refer to mBenchmarkMotifs
interaction_main_set	clean_MItab class, use this set of protein interactions to construct QSLIMFinder datasets
interaction_query_set	clean_MItab class, use this set of protein interactions as a query (+ add to the QSLIMFinder datasets). Both interaction sets have shared seed proteins. SLIMFinder analysis_type also requires this option because it add proteins from these interactions to the SLIMFinder datasets
analysis_type	"qslimfinder" or "slimfinder"
options	any options from QSLIMFinder or SLIMFinder. Detail http://rest.slimsuite.unsw.edu.au/docs&page=module:qslimfinder or http://rest.slimsuite.unsw.edu.au/docs&page=module:slimfinder => Commandline
domain_res_file	relative path to domain enrichment results RData
domain_results_obj	which object contains domain enrichment results in domain_res_file, XYZinteration_XZEmpiricalPval?
center_domains	logical, center QSLIMFinder datasets at domains?
filter_by_domain	logical, filter by domain? If FALSE this function does not use domain_res_file.
fasta_path	relative path (from the project folder) to the FASTA file containing sequences for all proteins in interaction_main_set and interaction_query_set
main_set_only	logical, If TRUE sequence sets for motif search contain only proteins from interaction_main_set. If FALSE, non-query proteins from interaction_query_set are also included. Argument for listInteractionSubsetFASTA
domain_pvalue_cutoff	construct SLIMFinder datasets using interactions of proteins that contain domain associated to protein in the query set with p-value domain_pvalue_cutoff or lower
SLIMFinder_dir	directory to store SLIMFinder datasets and results within the project directory
LSF_project_path	full path to the project directory
software_path	relative path (from the project folder) to the directory containing slimsuite, blast, iupred # "../software/cluster/" or "../software/"
length_set1_min	mininal number of proteins in a QSLIMFinder dataset from interaction_main_set. Argument for filterInteractionSubsetFASTA_list
length_set2_min	mininal number of proteins in a QSLIMFinder dataset from interaction_query_set. Argument for filterInteractionSubsetFASTA_list
write_log	FALSE will not allow runQSLIMFinder to detect crashed jobs
N_seq	number of sequences per batch
seed_list	character vector of UniprotKB accesions that should serve as a seed for QSLIMFinder datasets. These proteins are supposed to recognise SLIMs. Overrides selection of seed protein by domain_pvalue_cutoff
query_list	character vector of UniprotKB accesions that should serve as a query for QSLIMFinder
memory_start	integer, how much memory each job should be given initially
memory_step	interger, increment by which to increase how much memory each job should be given if memory_start is not enough and the job has failed
compare_motifs	logical, compare motifs using CompariMotif3? The procedure is relatively fast but memory consuming.
Njobs_limit	integer, the number of LSF jobs allowed to run simultaneously
CompariMotif3_dburl	dburl url where to download database for CompariMotif V3. Argument for runCompariMotif3
CompariMotif3_dbpath	path to directory where to save and keep ELM database (http://elm.eu.org/) or other database of linear motifs in a format required by comparimotif_V3: http://rest.slimsuite.unsw.edu.au/docs&page=module:comparimotif_V3
non_query_domain_res_file	path to RData file containing the result of domain enrichment analysis for non-query proteins
non_query_domain_results_obj	character, name of the object containing domain enrichment results for non-query proteins (class == XYZinteration_XZEmpiricalPval), when provided will be used for filtering datasets.
non_query_domains_N	the number of non-query proteins with predicted domains for each dataset. Used only when non_query_domain_results_obj is not NULL
non_query_set_only	If TRUE sequence sets for motif search contain only proteins (interacting partners of a seed) from non_query_domain_results_obj, if FALSE - both from non_query_domain_results_obj and domain_res_obj. Used only when non_query_domain_results_obj is not NULL and by default equals to main_set_only
query_domains_only	If TRUE proteins whose sequences will be used for motif search must be predicted to bind the same domains in a seed protein as domains predicted for query protein. Used only when non_query_domain_results_obj is not NULL

Details

QSLIMFinder command line options (http://rest.slimsuite.unsw.edu.au/docs&page=module:qslimfinder)

### Basic Input/Output Options ###

seqin=FILE : Sequence file to search [None]

batch=LIST : List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) [*.dat,*.fas]

query=LIST : Return only SLiMs that occur in 1+ Query sequences (Name/AccNum/Seq Number) [1]

addquery=FILE : Adds query sequence(s) to batch jobs from FILE [None]

maxseq=X : Maximum number of sequences to process [500]

maxupc=X : Maximum UPC size of dataset to process [0]

sizesort=X : Sorts batch files by size prior to running (+1 small->big; -1 big->small; 0 none) [0]

walltime=X : Time in hours before program will abort search and exit [1.0]

resfile=FILE : Main QSLiMFinder results table [qslimfinder.csv]

resdir=PATH : Redirect individual output files to specified directory (and look for intermediates) [QSLiMFinder/]

buildpath=PATH : Alternative path to look for existing intermediate files [SLiMFinder/]

force=T/F : Force re-running of BLAST, UPC generation and SLiMBuild [False]

pickup=T/F : Pick-up from aborted batch run by identifying datasets in resfile using RunID [False]

dna=T/F : Whether the sequences files are DNA rather than protein [False]

alphabet=LIST : List of characters to include in search (e.g. AAs or NTs) [default AA or NT codes]

megaslim=FILE : Make/use precomputed results for a proteome (FILE) in fasta format [None]

megablam=T/F : Whether to create and use all-by-all GABLAM results for (gablamdis) UPC generation [False]

ptmlist=LIST : List of PTM letters to add to alphabet for analysis and restrict PTM data []

ptmdata=DSVFILE : File containing PTM data, including AccNum, ModType, ModPos, ModAA, ModCode

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#

SLiMBuild Options I

efilter=T/F : Whether to use evolutionary filter [True]

blastf=T/F : Use BLAST Complexity filter when determining relationships [True]

blaste=X : BLAST e-value threshold for determining relationships [1e=4]

altdis=FILE : Alternative all by all distance matrix for relationships [None]

gablamdis=FILE : Alternative GABLAM results file [None] (!!!Experimental feature!!!)

homcut=X : Max number of homologues to allow (to reduce large multi-domain families) [0]

SLiMBuild Options II

masking=T/F : Master control switch to turn off all masking if False [True]

dismask=T/F : Whether to mask ordered regions (see rje_disorder for options) [False]

consmask=T/F : Whether to use relative conservation masking [False]

ftmask=LIST : UniProt features to mask out (True=EM,DOMAIN,TRANSMEM) []

imask=LIST : UniProt features to inversely ("inclusively") mask. (Seqs MUST have 1+ features) []

compmask=X,Y : Mask low complexity regions (same AA in X+ of Y consecutive aas) [5,8]

casemask=X : Mask Upper or Lower case [None]

motifmask=X : List (or file) of motifs to mask from input sequences []

metmask=T/F : Masks the N-terminal M (can be useful if termini=T) [True]

posmask=LIST : Masks list of position-specific aas, where list = pos1:aas,pos2:aas [2:A]

aamask=LIST : Masks list of AAs from all sequences (reduces alphabet) []

qregion=X,Y : Mask all but the region of the query from (and including) residue X to residue Y [0,-1]

SLiMBuild Options III

termini=T/F : Whether to add termini characters (^ & $) to search sequences [True]

minwild=X : Minimum number of consecutive wildcard positions to allow [0]

maxwild=X : Maximum number of consecutive wildcard positions to allow [2]

slimlen=X : Maximum length of SLiMs to return (no. non-wildcard positions) [5]

minocc=X : Minimum number of unrelated occurrences for returned SLiMs. (Proportion of UP if < 1) [0.05]

absmin=X : Used if minocc<1 to define absolute min. UP occ [3]

alphahelix=T/F : Special i, i+3/4, i+7 motif discovery [False]

SLiMBuild Options IV

ambiguity=T/F : (preamb=T/F) Whether to search for ambiguous motifs during motif discovery [True]

ambocc=X : Min. UP occurrence for subvariants of ambiguous motifs (minocc if 0 or > minocc) [0.05]

absminamb=X : Used if ambocc<1 to define absolute min. UP occ [2]

equiv=LIST : List (or file) of TEIRESIAS-style ambiguities to use [AGS,ILMVF,FYW,FYH,KRH,DE,ST]

wildvar=T/F : Whether to allow variable length wildcards [True]

combamb=T/F : Whether to search for combined amino acid degeneracy and variable wildcards [False]

SLiMBuild Options V

musthave=LIST : Returned motifs must contain one or more of the AAs in LIST (reduces search space) []

focus=FILE : FILE containing focal groups for SLiM return (see Manual for details) [None]

focusocc=X : Motif must appear in X+ focus groups (0 = all) [0]

* See also rje_slimcalc options for occurrence-based calculations and filtering *

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#

### SLiMChance Options ###

cloudfix=T/F : Restrict output to clouds with 1+ fixed motif (recommended) [False]

slimchance=T/F : Execute main QSLiMFinder probability method and outputs [True]

sigprime=T/F : Calculate more precise (but more computationally intensive) statistical model [False]

sigv=T/F : Use the more precise (but more computationally intensive) fix to mean UPC probability [False]

qexact=T/F : Calculate exact Query motif space (True) or over-estimate from dimers (False) (quicker) [True]

probcut=X : Probability cut-off for returned motifs [0.1]

maskfreq=T/F : Whether to use masked AA Frequencies (True), or (False) mask after frequency calculations [False]

aafreq=FILE : Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) [None]

aadimerfreq=FILE: Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) (!!!Experimental!!!) [None]

negatives=FILE : Multiply raw probabilities by under-representation in FILE (!!!Experimental!!!) [None]

smearfreq=T/F : Whether to "smear" AA frequencies across UPC rather than keep separate AAFreqs [False]

seqocc=T/F : Whether to upweight for multiple occurrences in same sequence (heuristic) [False]

probscore=X : Score to be used for probability cut-off and ranking (Prob/Sig) [Sig]

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#

Advanced Output Options I

clouds=X : Identifies motif "clouds" which overlap at 2+ positions in X+ sequences (0=minocc / -1=off) [2]

runid=X : Run ID for resfile (allows multiple runs on same data) [DATE:TIME]

logmask=T/F : Whether to log the masking of individual sequences [True]

slimcheck=FILE : Motif file/list to add to resfile output []

Advanced Output Options II

teiresias=T/F : Replace TEIRESIAS, making *.out and *.mask.fasta files [False]

slimdisc=T/F : Emulate SLiMDisc output format (*.rank & *.dat.rank + TEIRESIAS *.out & *.fasta) [False]

extras=X : Whether to generate additional output files (alignments etc.) [1]

–1 = No output beyond main results file

- 0 = Generate occurrence file and cloud file

- 1 = Generate occurrence file, alignments and cloud file

- 2 = Generate all additional QSLiMFinder outputs

- 3 = Generate SLiMDisc emulation too (equiv extras=2 slimdisc=T)

targz=T/F : Whether to tar and zip dataset result files (UNIX only) [False]

savespace=0 : Delete "unneccessary" files following run (best used with targz): [0]

- 0 = Delete no files

- 1 = Delete all bar *.upc and *.pickle

- 2 = Delete all bar *.upc (pickle added to tar)

- 3 = Delete all dataset-specific files including *.upc and *.pickle (not *.tar.gz)

Advanced Output Options III

topranks=X : Will only output top X motifs meeting probcut [1000]

minic=X : Minimum information content for returned motifs [2.1]

allsig=T/F : Whether to also output all SLiMChance combinations (Sig/SigV/SigPrime/SigPrimeV) [False]

Memory requirements for jobs. How much memory is enough for most jobs? files = list.files("./qslimfinder.Full_IntAct.FALSE/log_dir/log/") times = sapply(files, function(file) system(paste0("cat ./qslimfinder.Full_IntAct.FALSE/log_dir/log/",file," | grep Requested"), intern = T)) > table(times) times 100.00 MB 200.00 MB 300.00 MB 400.00 MB 500.00 MB 14 61 53 25 3 > table(times) / sum(table(times)) times 100.00 MB 200.00 MB 300.00 MB 400.00 MB 500.00 MB 0.08974359 0.39102564 0.33974359 0.16025641 0.01923077 > cumsum(table(times) / sum(table(times))) 100.00 MB 200.00 MB 300.00 MB 400.00 MB 500.00 MB 0.08974359 0.48076923 0.82051282 0.98076923 1.00000000 > 1 - cumsum(table(times) / sum(table(times))) 100.00 MB 200.00 MB 300.00 MB 400.00 MB 500.00 MB 0.91025641 0.51923077 0.17948718 0.01923077 0.00000000

Value

path to RData containing all objects used by this pipeline

Author(s)

Vitalii Kleshchevnikov

See Also

listInteractionSubsetFASTA, runQSLIMFinder, groupQSLIMFinderCommand, mQSLIMFinderCommand, runCompariMotif3, readQSLIMFinderMain, readQSLIMFinderOccurence, writeInteractionSubsetFASTA_list, domainProteinPairMatch, filterInteractionSubsetFASTA_list, removeInteractionNoFASTA, centerDomains

vitkl/SLIMFinderR documentation built on May 3, 2019, 8:08 p.m.