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Option Type: boolean

Argument: abschg ac accnr acconly addbaits addclass addimports addlinks addqueries addrand addscore addtags adduni advprob ailmv aliases align alliso allowvar allquery allsig alltypes alnstats alphahelix altft altpos ambiguity analyse aname anchors annotate append aromatic asscombo assembly association autofilter autoload autorun autoskip backup backups balanced balchg batchbase batchmode benchmark bestmatch bestorf biallelic bigfirst bigindex blanks blastann blastcf blastf blastforce blastg blastgen bootweight branchlen bysmrt calculate calls casefilter cc2ft cdsonly chaser checknum checktype checktypes chromalign cleandb cleanhaq cleanres cleanup cleardata clearhtml clonemap cloudfix clusterfas clusters codons colbydeg combamb combcut combine combinedfas combineppi compare compfilter compile complete complexfas compresspp concatenate consamb consensi consinfo consmask consout coreic countspec coverage cyscount cysweight cytoscape datindex datout dbcomp dbdetails dbindex dbonly dbsizes dbsplit debug degap depthplot desconly dev dimfreq diploid dirsum disgraph dismask dismat dismatrix distrees dna dnds domainfas domains dombench domlink domppi domtable dotplots download dropout edithome efilter elmbench empai ensdat ensfilter ensloci enspep eorf es est2haq est2rf estgen expand expect exponly extendaa extract extras fakehtml fakemask fasout fiestacons fillcol filterself filterseq fixdown fixlen fixup flatout foldindex force formatdb fragfas fragment fragrevcomp frapout ftout fudgeft fullblast fulldoc fullens fullforce fullhgnc fullmap fullnr fulloutput fullpath fullrbh fullref fullres fullscramble fupc fwdonly gablam gablamout gabrev gabsim gapblast gapfilter genecards genelists generate genesummary genetar globid gnspacc gopher gopherfam gosummary gotable grepdat gspcode gzip haircut halfhap haq haqbatch haqesac header help hgnconly hitsum hmmcalibrate hmmpfam homfilter hostvirus hprdfas href html htmlall hubonly hubs ignoredate ignoren ignoreref indels index integrity inversedb invmask iridis iterate itraq iuchdir iupred jackknife keep keepblast keeplocal keepnames keepnew keeporder kimura legacy lencorrect loadbalance local localalnfas localsAM localunique locusout logfork logint logmask logrem longlink longtdt mailstart mains majdif majfocus majmut majref makefas makeflyseq makehtml makeindex makejim makepages makepng makesnp makespec makeuniprot manpaq mansaq mapfas mapout maptomany markov maskcleave maskfreq masking maskpickle matchic mcode megablam megaslimfix memsaver mergesplits metmask minimotif mitab mixed modpurge monophyly monster motifaln motific motifs motinfo msms multiclass multicut multihaq mysql naturaljoin netchg newlog noamb nobots nocomplex nocontrols nocopyfas nodeonly noforks nohits noquery noshare nosplice noutr nralign nrfastq nrgen nrkeepann nrmotif nrpep nrsamespec nrseq nsf2nwk nterm obsgo occbench occonly occupc oldblast oldmonster oldscores onetomany optimise ordered orderedfas orfmet organise orphan orphans osx overlap overlaps palindrome pamtree paq parafam paralign parameters parasplice partial patisfas pepmwt peptides percres phaseindels phos phosdat picids pickall pickid pickle pickleout pickup plurals poolgen posinfo postdup ppextra ppibench ppidbreport ppifas ppisym ppitab predict prepaq proteinaln proteins protscores protsummary pround pureapi purify qassemble qassemblefas qcomplete qexact qryacc qrygaps qryvar qspec qsub queries querynr ranbench randat randdesc randomise rank rankfilter ranking rankonly readlen recase reciprocal recloud redundancy relgappen rename replacechar report rescale restout restrict results revcompnr reverse revertnr reviewed rgraphics rid rjepy rmdirs rna2dna rqmean rsh runfield saq savespace saveupc savexref scaled scap scavenge scramble screenens screenipi screenqry screenrev seedfreq self selfhit selfonly selfsum seqbyseq seqcluster seqfiles seqfilter seqindex seqnr seqnum seqocc seqshuffle seqstats seqwt sgd2sp sigprime sigv silent simbench simulate singletons skipdormant skipknown skipquiet slimbuild slimchance slimchg slimcons slimdisc slimfold slimhyd slimiup slimjim slimmaker slimppi slimprob slimquery slimsa slimsuite smearfreq snapper snpbyftype snponly snptable snptableout soaplab softmask sorted sortrun sortxref specnr speconly spectable speedskip splicego splicevar splitcsv spokes sticky stickyhubs stickyppi strict stripnum subdir subfolders summarise summaryhgnc svg symmetric symmetry tableonly tabout targz teiresias termini test tidy tidygap tmconvert tofile tophtml torf toscreen trimtrunc trimx truncnt tryparent txt unihtml unionly uniquexref unitab unkspec unmatched update updatepos usealn usebeta usecase usedate usego usegopher usehome usenandr usepos useres usespec useweb varlength vgablam vgbparse vspcode warn webobo webserver weighted wildscram wildvar win32 xgcomplex xgformat xgmml xhubppi xmerocc xreformat xreftab zfilter zscore

Modules: bob extatic humsf09 jrj_fastq orcfinder patis revert rje_aic rje_archive rje_embl rje_gquad rje_hm_html rje_hmm_V2 rje_mirna rje_pacbio rje_paml rje_price rje_slimfungo rje_taxamap samphaser scap slimfrap slimjim spydarm trex compass file_monster pic_html prodigis rje_dbase rje_glossary rje_itunes rje_mysql rje_pattern_discovery rje_phos rje_pydocs rje_seqgen rje_seqplot rje_sleeper rje_yeast seqforker slim_pickings gopher_V2 qslimfinder_V1.9 slimbench_V1 slimfinder_V4.9 slimprob_V1.4 rje_ancseq rje_biogrid rje_blast_V1 rje_blast_V2 rje_blast rje_conseq rje_db rje_dismatrix_V2 rje_dismatrix_V3 rje_disorder rje_ensembl rje_forker rje_genbank rje_genecards rje_genemap rje_go rje_haq rje_hmm_V1 rje_hpc rje_hprd rje_html rje_iridis rje_markov rje_mascot rje_mitab rje_motiflist rje_motif_V3 rje_obj rje_ppi rje_qsub rje_samtools_V0 rje_samtools rje_seqlist rje_seq rje_slimcalc rje_slimcore rje_slimhtml rje_slimlist rje_slim rje_synteny rje_taxonomy rje_tm rje_tree rje_uniprot rje rje_xref snp_mapper aphid badasp budapest comparimotif_V3 fiesta gablam gfessa gopher happi haqesac multihaq pagsat_V1 pagsat peptcluster pingu_V3 pingu_V4 presto_V5 qslimfinder seqmapper seqsuite slimbench slimfarmer slimfinder slimmaker slimmutant slimparser slimprob slimsearch slimsuite smrtscape_V1 smrtscape snapper unifake

ModuleOptionDescriptionDefault
aphid blanks=T/F Whether to include most blank enrichment/jacknife rows for missing NRID True
aphid flatout=T/F Whether to output reduced GeneMap flatfiles (*.data.tdt & *.aliases.tdt) False
aphid force=T/F Regenerate intermediate files even if found False
aphid jackknife=T/F Whether to perform jack-knifing tests on enrpairs True
aphid logint=T/F Whether intensity value is a log intensity True
badasp allowvar=T/F Allow variants of same species within a group. False
badasp desconly=T/F Limits ancestral AAs to those found in descendants True
badasp fixdown=T/F Fix AAs on initial pass down tree False
badasp fixup=T/F Fix AAs on way up (keep probabilities) True
badasp gnspacc=T/F Convert sequences into gene_SPECIES__AccNum format wherever possible. True
badasp newlog=T/F Create new log file. Default = False: append log file
badasp ordered=T/F Order ancestral sequence output by node number False
badasp orphan=T/F Whether orphans sequences (not in subfam) allowed. True
badasp pamtree=T/F Calculate and output ancestral tree with PAM distances True
badasp rank=T/F Whether to output ranks as well as scores True
badasp trimtrunc=T/F Whether to trim the leading and trailing gaps (within groups) -> change to X False
badasp win32=T/F Run in Win32 Mode False
bob recloud=T/F Whether to try to recloud motifs once filtered True
budapest cleanhaq=T/F Delete excessive HAQESAC results files True
budapest clusterfas=T/F Generate fasta files of translations and BLAST hits in NR clusters False
budapest empai=T/F Whether emPAI data is present in MASCOT file True
budapest fiestacons=T/F Use FIESTA to auto-construct consensi from BUDAPEST RF translations True
budapest fwdonly=T/F Whether to treat EST/cDNA sequences as coding strands (False = search all 6RF) False
budapest gnspacc=T/F Convert sequences into gene_SPECIES__AccNum format wherever possible. True
budapest haqesac=T/F HAQESAC analysis of identified EST translations True
budapest itraq=T/F Whether data is from an iTRAQ experiment False
budapest multihaq=T/F Whether to run HAQESAC in two-phases with second, manual phase False
budapest partial=T/F Whether partial EST data is acceptable (True) or all MASCOT hits must be found (False) True
budapest seqcluster=T/F Perform additional sequence (BLAST/GABLAM) clustering True
comparimotif_V3 coreic=T/F Whether to output normalised Core IC True
comparimotif_V3 dna=T/F Whether motifs should be considered as DNA motifs False
comparimotif_V3 memsaver=T/F Run in more efficient memory saver mode. XGMML output not available. False
comparimotif_V3 motific=T/F Output Information Content for motifs False
comparimotif_V3 nrmotif=T/F Whether to remove redundancy in input motifs False
comparimotif_V3 overlaps=T/F Whether to include overlapping ambiguities (e.g. [KR] vs [HK]) as match True
comparimotif_V3 pickle=T/F Whether to load/save pickle following motif loading/filtering False
comparimotif_V3 reverse=T/F Reverse the input motifs. False
comparimotif_V3 trimx=T/F Trims Xs from the ends of a motif False
comparimotif_V3 unmatched=T/F Whether to output lists of unmatched motifs (not from searchdb) into *.unmatched.txt False
comparimotif_V3 xgformat=T/F Whether to use default CompariMotif formatting or leave blank for e.g. Cytoscape True
comparimotif_V3 xgmml=T/F Whether to output XGMML format results True
compass autorun=T/F Automated querying of web servers (within RCSI only) False
compass partial=T/F Allow partial scansite results (NULL values) False
compass recase=T/F Whether to look for accession numbers in case-independent fashion (scansite results) True
compass results=T/F Whether to output summary file or simply check/generate results (Aligned seqs only) True
compass txt=T/F Whether to look by deafult for *.server.txt files (True) or *.server files (False) True
extatic cdsonly=T/F Whether to restrict analysis to cDNA with matching CDS True
extatic fullnr=T/F Perfrom NR Flank analysis across all genes False
fiesta annotate=T/F Annotate consensus sequences using BLAST-based approach False
fiesta assembly=T/F Assemble EST sequences prior to search False
fiesta bestorf=T/F Whether to use the "Best" ORF only for ESTs without BLAST Hits True
fiesta blastann=T/F Execute BLAST-based annotation of conensus translations only, on seqin False
fiesta cleanhaq=T/F Delete excessive HAQESAC results files True
fiesta consensi=T/F Assemble hit ORF into consensus sequences False
fiesta dna=T/F Implement DNA-based GABLAM assembly True
fiesta est2haq=T/F Execute BLAST-based EST to RF translation/annotation on seqin followed by HAQESAC analysis False
fiesta est2rf=T/F Execute BLAST-based EST to RF translation/annotation only, on seqin False
fiesta fwdonly=T/F Whether to treat EST/cDNA sequences as coding strands (False = search all 6RF) False
fiesta gabrev=T/F Whether to use GABLAM-based reverse complementation True
fiesta gapblast=T/F Whether to allow gaps during BLAST identification of GABLAM homologues False
fiesta gnspacc=T/F Convert sequences into gene_SPECIES__AccNum format wherever possible. False
fiesta haqbatch=T/F Whether to only generate HAQESAC batch file (True) or perform whole run (False) False
fiesta haqesac=T/F HAQESAC analysis of identified EST translations True
fiesta multihaq=T/F Whether to run HAQESAC in two-phases True
fiesta pickup=T/F Whether to read in partial results and skip those sequences True
fiesta truncnt=T/F Whether to truncate N-terminal to Met in final BLAST annotation (if hit) False
file_monster cleanup=T/F Whether to delete empty directories (and move/delete stripnum) False
file_monster dirsum=T/F Whether to perform summary of directory contents False
file_monster dirsum=T/F Whether to perform summary of directory contents False
file_monster keepnew=T/F Preferentially keep newer files of same size if good/bad status equal True
file_monster monster=T/F Whether to perform monster cleanup of redundant files False
file_monster oldmonster=T/F Whether to run old File Monster (V1.x). Will be retired once update complete. False
file_monster redundancy=T/F Whether to check/rate redundancy for scavenge etc. True
file_monster rename=T/F Whether to rename files False
file_monster scavenge=T/F Whether to perform collation of file information False
file_monster scavenge=T/F Whether to perform collation of file information False
file_monster stripnum=T/F Whether files may have -XXX numerical suffix from renaming, which should be stripped False
file_monster subfolders=T/F Whether to look in subfolders True
file_monster subfolders=T/F Whether to look in subfolders True
file_monster usedate=T/F Whether to use date in new name False
gablam alnstats=T/F Whether to output GABLAM stats or limit to one-line stats (blastb=0) True
gablam append=T/F Whether to append to output file or not. (Not available for blastres=FILE or fullblast=F) False
gablam blastf=T/F Complexity Filter (BLAST -F X) False
gablam checktype=T/F Whether to check sequence types and BLAST program selection True
gablam clusters=T/F Whether to output a list of clusters based on shared BLAST homology True
gablam combinedfas=T/F Whether to generate a combined fasta file False
gablam disgraph=T/F Whether to output a graph representation of the distance matrix (edges = homology) False
gablam dismat=T/F Whether to output compiled distance matrix True
gablam distrees=T/F Whether to generate UPGMA tree summaries of all-by-all distances True
gablam dotplots=T/F Whether to use gablam.r to output dotplots. (Needs R installed and setup) False
gablam fasout=T/F Output a fasta file per input sequence "ACCNUM.DBASE.fas" False
gablam fragfas=T/F Whether to output fragmented Hits based on local alignments False
gablam fragrevcomp=T/F Whether to reverse-complement DNA fragments that are on reverse strand to query True
gablam fullblast=T/F Whether to perform full BLAST followed by blastres analysis True
gablam fullres=T/F Whether to output full GABLAM results table True
gablam globid=T/F Whether to output Global %ID using ALIGN False
gablam hitsum=T/F Whether to output the BLAST Hit Summary table True
gablam keepblast=T/F Whether to keep the blast results files rather than delete them True
gablam local=T/F Whether to output local alignment summary stats table True
gablam localalnfas=T/F Whether to output local alignments to *.local.fas fasta file (if local=T) False
gablam localsAM=T/F Save local (and unique) hits data as SAM files in addition to TDT False
gablam localunique=T/F Reduce local hits to unique non-overlapping regions (*.unique.tdt) snptable=T/F
gablam mysql=T/F Whether to output column headers for mysql table build False
gablam noforks=T/F Whether to avoid forks False
gablam nrsamespec=T/F Non-Redundancy within same species only. False
gablam nrseq=T/F Make sequences Non-Redundant following all-by-all. False
gablam percres=T/F Whether output is a percentage figures (2d.p.) or absolute numbers True
gablam posinfo=T/F Output the Start/End limits of the BLAST Hits True
gablam qassemble=T/F Whether to fully assemble query stats from all hits in HitSum False
gablam qryacc=T/F Whether to use the Accession Number rather than the short name for the Query True
gablam saveupc=T/F Whether to output a UPC file for SLiMSuite compatibility False
gablam selfhit=T/F Whether to include self hits in the fullres output True
gablam selfsum=T/F Whether to also include self hits in hitsum output False
gablam singletons=T/F Whether to include singleton in main tree and distance matrix False
gablam snptable=T/F Generate a SNP table (similar to MUMmer NUCmer output) for query/hit overlap (fullblast=T) False
gfessa bestmatch=T/F Whether to stop looking for more mismatches once hits of a given stringency found True
gfessa expand=T/F Whether to expand from enriched TAGs to unenriched TAGs through shared sequence hits True
gfessa longtdt=T/F Whether to output "Long" format file needed for R analysis True
gopher compfilter=T/F Whether to use complexity filter and composition statistics for *initial* BLAST True
gopher dna=T/F Whether to analyse DNA sequences (not optimised) False
gopher dropout=T/F Whether to "drop out" at earlier phases, or continue with single sequence False
gopher force=T/F Whether to force execution at current level even if results are new enough False
gopher fullforce=T/F Whether to force current and previous execution even if results are new enough False
gopher fullforce=T/F Whether to force current and previous execution even if results are new enough False
gopher fullrbh=T/F Whether RBH method should run BLAST searches for all potential RBH orthologues False
gopher gopherfam=T/F Whether to combined paralogous gopher orthologues into protein families (>minsim) (assuming run to orthfas+) False
gopher ignoredate=T/F Ignores the age of files and only replaces if missing False
gopher ignoredate=T/F Ignores the age of files and only replaces if missing False
gopher oldblast=T/F Run with old BLAST rather than BLAST+ False
gopher organise=T/F Output files according to orthdb an species (code or TaxaID - need conversion) True
gopher parafam=T/F Whether to paralogue paired subfamily alignments (>minsim) (assuming run to orthfas+) False
gopher paralign=T/F Whether to produce paralogue alignments (>minsim) in PARALN/ (assuming run to orthfas+) False
gopher parasplice=T/F Whether splice variants (where identified) are counted as paralogues False
gopher postdup=T/F Whether to align only post-duplication sequences False
gopher reciprocal=T/F Use Reciprocal Best Hit method instead of standard GOPHER approach False
gopher savespace=T/F Save space by deleting intermediate blast files during orthfas True
gopher sticky=T/F Switch on "Sticky Orthologous Group generation" False
gopher_V2 dna=T/F Whether to analyse DNA sequences (not optimised) False
gopher_V2 dropout=T/F Whether to "drop out" at earlier phases, or continue with single sequence False
gopher_V2 force=T/F Whether to force execution at current level even if results are new enough False
gopher_V2 fullforce=T/F Whether to force current and previous execution even if results are new enough False
gopher_V2 gopherfam=T/F Whether to combined paralogous gopher orthologues into protein families (>minsim) (assuming run to orthfas+) False
gopher_V2 ignoredate=T/F Ignores the age of files and only replaces if missing False
gopher_V2 ignoredate=T/F Ignores the age of files and only replaces if missing False
gopher_V2 parafam=T/F Whether to paralogue paired subfamily alignments (>minsim) (assuming run to orthfas+) False
gopher_V2 paralign=T/F Whether to produce paralogue alignments (>minsim) in PARALN/ (assuming run to orthfas+) False
gopher_V2 parasplice=T/F Whether splice variants (where identified) are counted as paralogues False
gopher_V2 postdup=T/F Whether to align only post-duplication sequences False
gopher_V2 reciprocal=T/F Use Reciprocal Best Hit method instead of standard GOPHER approach False
gopher_V2 savespace=T/F Save space by deleting intermediate blast files during orthfas True
gopher_V2 sticky=T/F Switch on "Sticky Orthologous Group generation" False
happi addclass=T/F Whether to add the Classes themselves to the PPI networks as nodes False
happi fillcol=T/F Fill in colour for missing class combinations True
happi makepng=T/F Whether to (look for and) make PNG files with R True
happi multiclass=T/F Whether to allow membership of multiple classes (joined by "-" True
happi nobots=T/F Whether to insert no-bot meta tag to pages True
happi ppextra=T/F Make additional pages for genes added and returned in MCODE clusters False
happi svg=T/F Use SVG files instead of PNG files True
happi updatepos=T/F Whether to run an additional round of the layout algorithm if npos found False
happi usepos=T/F Whether to use existing Node positions if found True
happi xgmml=T/F Whether to also output XGMML files in PNG/SVG directories False
happi xreftab=T/F Add database cross-reference tabs to the front page Class tabs True
haqesac ac=T/F Ancestor Construction (GASP) True
haqesac accnr=T/F Check for redundant Accession Numbers/Names on loading sequences. False
haqesac allowvar=T/F Allow variants of same species within a group. False
haqesac backup=T/F Whether to backup initial fasta file. Will overwrite existing *.fas.bak. True
haqesac blastf=T/F Complexity Filter (BLAST -F X) True
haqesac cleanup=T/F Initial data cleanup True
haqesac dbonly=T/F Whether to only allow sequences from listed databases False
haqesac desconly=T/F Limits ancestral AAs to those found in descendants True
haqesac es=T/F Establishment of Subfamilies True
haqesac fixdown=T/F Fix AAs on initial pass down tree False
haqesac fixup=T/F Fix AAs on way up (keep probabilities) True
haqesac gablam=T/F Whether to use GABLAMO Global Alignment from BLAST Local Alignment Matrix (Ordered) rather than ALIGN True
haqesac gabsim=T/F Whether to use %Similarity for GABLAMO comparisons, rather than %Identity True
haqesac gnspacc=T/F Convert sequences into gene_SPECIES__AccNum format wherever possible. True
haqesac haq=T/F Homologue Alignment Quality True
haqesac keep=T/F Keep all sequences (saqkl=0, paqkl=0) False
haqesac manpaq=T/F Manual over-ride of sequence rejection decisions in PAQ False
haqesac mansaq=T/F Manual over-ride of sequence rejection decisions in SAQ False
haqesac multihaq=T/F If pickle present, will load and continue, else will part run then pickle and stop False
haqesac newlog=T/F Create new log file. Default = False: append log file
haqesac noquery=T/F No Query for SAQ, Random Query for PAQ (else query=X or first sequence) False
haqesac ordered=T/F Order ancestral sequence output by node number False
haqesac orphan=T/F Whether orphans sequences (not in subfam) allowed. True
haqesac pamtree=T/F Calculate and output ancestral tree with PAM distances True
haqesac paq=T/F Pairwise AQ True
haqesac prepaq=T/F PrePAQ tree grouping True
haqesac qryvar=T/F Keep variants of query species within a group (over-rides allowvar=F). False
haqesac qspec=T/F Whether to highlight query species in PNG tree files True
haqesac saq=T/F Single Sequence AQ True
haqesac seqnr=T/F Make sequence Non-Redundant True
haqesac specnr=T/F Non-Redundancy within same species only True
haqesac unkspec=T/F Whether sequences of unknown species are allowed True
haqesac usealn=T/F Use current alignment (do not realign, degap=F) False
humsf09 annotate=T/F Whether to manually annotate/classify SLiMs False
humsf09 frapout=T/F Whether to generate SLiMFRAP 0.0 output tables False
humsf09 seqwt=T/F Perform SeqWt FDR calculations True
humsf09 skipknown=T/F Whether to skip known SLiMs in manual annotation (True), or ask to check (False) False
humsf09 slimjim=T/F Whether to process data for SLiMJIM output True
humsf09 usego=T/F Whether to use GO datasets False
humsf09 usenandr=T/F Whether to use Neduva & Russell results False
jrj_fastq nrfastq=T/F Remove redundant sequences (based on names) False
multihaq addqueries=T/F Whether to add query database to blast2fas list True
multihaq autoskip=T/F Whether to automatically skip queries found in previous runs False
multihaq chaser=T/F Option for running second phase of multihaq as second run whilst first run in progress False
multihaq force=T/F Whether to force re-running of stages (True) or pick-up pre-existing runs (False) False
multihaq haqesac=T/F Run HAQESAC (True) or limit to batch file output (False) True
multihaq keepblast=T/F Whether to keep BLAST results files True
multihaq multihaq=T/F Whether to run HAQESAC in two-phase multihaq mode True
multihaq screenqry=T/F Whether to look for queries in previous runs and give option to skip True
orcfinder blastf=T/F Use BLAST Complexity filter when determining relationships True
orcfinder efilter=T/F Whether to use evolutionary filter True
orcfinder force=T/F Force re-running of BLAST, UPC generation and SLiMBuild False
orcfinder pickup=T/F Pick-up from aborted batch run by identifying last dataset output in resfile False
pagsat casefilter=T/F Whether to filter leading/trailing lower case (low QV) sequences True
pagsat chromalign=T/F [Discontinued] Whether to perform crude chromosome-contig alignment False
pagsat diploid=T/F Whether to treat assembly as a diploid False
pagsat dismatrix=T/F Whether to generate distance matrix of chromosome vs contig identities False
pagsat dotplots=T/F Whether to use gablam.r to output dotplots for all ref vs assembly. False
pagsat genesummary=T/F Whether to include reference gene searches in summary data True
pagsat genetar=T/F Whether to tar and zip the GeneHits/ and ProtHits/ folders (if generated & Mac/Linux) True
pagsat makesnp=T Generate the full set of SNP outputs for Snapper False
pagsat mapfas=T/F Output assembly *.map.fasta file with RevComp contigs based on initial (automatic) mapping True
pagsat orderedfas=T/F Whether to generate crude ordered contig output for e.g. Progressive Mauve False
pagsat orphans=T/F Whether to include and process orphan contigs True
pagsat protsummary=T/F Whether to include reference protein searches in summary data True
pagsat report=T/F Whether to generate HTML report True
pagsat rgraphics=T/F Whether to generate PNG graphics using R. (Needs R installed and setup) True
pagsat snapper=T/F Run Snapper to generate "best" unique mapping of assembly contigs to Reference True
pagsat tidy=T/F Execute semi-automated assembly tidy/edit mode to complete draft assembly False
pagsat_V1 casefilter=T/F Whether to filter leading/trailing lower case (low QV) sequences True
pagsat_V1 chromalign=T/F Whether to perform crude chromosome-contig alignment True
pagsat_V1 diploid=T/F Whether to treat assembly as a diploid False
pagsat_V1 dotplots=T/F Whether to use gablam.r to output dotplots for all ref vs assembly. False
pagsat_V1 genesummary=T/F Whether to include reference gene searches in summary data True
pagsat_V1 genetar=T/F Whether to tar and zip the GeneHits/ and ProtHits/ folders (if generated & Mac/Linux) True
pagsat_V1 orphans=T/F Whether to include and process orphan contigs True
pagsat_V1 protsummary=T/F Whether to include reference protein searches in summary data True
pagsat_V1 report=T/F Whether to generate HTML report True
pagsat_V1 rgraphics=T/F Whether to generate PNG graphics using R. (Needs R installed and setup) True
pagsat_V1 snapper=T/F Run Snapper on ctidX/haploid output following PAGSAT Tidy. (Re-Quiver recommended first.) False
pagsat_V1 tidy=T/F Execute semi-automated assembly tidy/edit mode to complete draft assembly False
patis clonemap=T/F Whether to map clones onto sequence file and check RE sites etc. False
patis eorf=T/F Whether to consider eORFs True
patis patisfas=T/F Whether to output PATIS fasta file with extensions and AIC marked True
patis torf=T/F Whether to consider tORFs True
peptcluster termini=T/F Whether peptides for alignment have termini (^ & $) or X flanking regex match True
pic_html clearhtml=T/F Delete existing HTML in picture folders (*.htm and *.html) - may overwrite anyway. True
pic_html edithome=T/F Whether to regenerate the pictures home page True
pic_html picids=T/F Whether pictures have picture IDs 'ID - Name.*' True
pic_html usehome=T/F Whether to extract descriptions etc. from the pictures home page True
pingu_V3 acconly=T/F Whether to output lists of Accession numbers only, rather than full fasta files False
pingu_V3 addbaits=T/F Whether to add primary interactors of baits as additional samples False
pingu_V3 addlinks=T/F Add linking proteins (linking two Sample proteins) False
pingu_V3 asscombo=T/F Whether to subdivide genes further based on combinations of experiments containing them False
pingu_V3 association=T/F Perform experiment association analysis False
pingu_V3 compresspp=T/F Whether to compress multiple samples of interest into ShareX for cytoscape False
pingu_V3 cytoscape=T/F Produce old cytoscape input files from allbyall table (reads back in) False
pingu_V3 dbcomp=T/F Comparison of PPI databases False
pingu_V3 dbsizes=T/F Outputs a file of PPI dataset sizes (histogram) False
pingu_V3 exponly=T/F Limited analysis to samples listed as experiments (before baits added etc.) False
pingu_V3 fulloutput=T/F Generate all possible outputs from one input False
pingu_V3 gablam=T/F Whether to run all-by-all GABLAM on EnsLoci and add homology to networks True
pingu_V3 genelists=T/F Generate lists of genes for each sample (e.g. for FatiGO upload) False
pingu_V3 gosummary=T/F Make a GO summary table False
pingu_V3 hgnconly=T/F Whether to restrict PPI data to only those proteins with Gene Symbol links False
pingu_V3 mapout=T/F Generate a summary table of full peptide mapping False
pingu_V3 nocomplex=T/F Perform crude screening of complexes (PPI triplets w/o homodimers) False
pingu_V3 nocontrols=T/F Whether to remove genes found in designated controls from designated experiments False
pingu_V3 noshare=T/F Whether to exclude those genes that are shared between samples when comparing those samples True
pingu_V3 overlap=T/F Produce a table of the overlap (mapped through HGNC) between samples (and bait 1y PPI) False
pingu_V3 pickle=T/F Whether to save/load pickle of parsed/combined data rather than regenerating each time True
pingu_V3 selfonly=T/F Whether to only look at associations within experiments, not between False
pingu_V3 seqfiles=T/F Whether to generate protein sequence fasta files using EnsLoci False
pingu_V3 stickyhubs=T/F Only remove "sticky" spokes but keep sticky hubs False
pingu_V3 stickyppi=T/F Only remove "sticky" hubs from samples, not from total PPI False
pingu_V3 summaryhgnc=T/F Generate a summary table of genes in dataset, including peptide lists for each sample False
pingu_V3 xgcomplex=T/F Restrict XGMML output (and expansion) to protein complex edges False
pingu_V3 xgformat=T/F Whether to add colour/shape formatting to XGMML output False
pingu_V3 xgmml=T/F Produce an XGMML file with all Cytoscape data and more False
pingu_V4 acconly=T/F Whether to output lists of Accession numbers only, rather than full fasta files False
pingu_V4 allquery=T/F Whether to include all the new Queries from QueryPPI in all files for a given hub True
pingu_V4 combineppi=T/F Whether to combine all spokes into a single fasta file False
pingu_V4 domppi=T/F Whether to generate Pfam Domain-based PPI files instead of protein-based PPI files False
pingu_V4 download=T/F Whether to download files directly from websites where possible if missing True
pingu_V4 hubonly=T/F Whether to restrict pairwise PPI to those with both hub and spoke in hublist False
pingu_V4 integrity=T/F Whether to quit by default if source data integrity is breached True
pingu_V4 ppidbreport=T/F Summary output for PPI compilation of evidence/PPIType/DB overlaps True
pingu_V4 ppifas=T/F Whether to output PPI fasta files False
pingu_V4 symmetry=T/F Whether to enforce Hub-Spoke symmetry during PPI compilation True
pingu_V4 xhubppi=T/F Whether to generate PPI files of spokes interacting with X+ hubs False
presto_V5 compare=T/F Compare the motifs from the motifs FILE with the searchdb FILE (or self if None) False
presto_V5 consamb=T/F Whether to calculate conservation allowing for degeneracy of motif (True) or of fixed variant (False) True
presto_V5 consinfo=T/F Weight positions by information content (does nothing for conscore=abs) True
presto_V5 consout=T/F Outputs an additional result field containing information on the conservation score used False
presto_V5 datout=T/F Whether to output hits as a uniprot format file *.uniprot.presto False
presto_V5 expect=T/F Whether to give crude expect values based on AA frequencies True
presto_V5 fasout=T/F Whether to output hit sequences as a fasta format file motif.fas False
presto_V5 foldindex=T/F Run FoldIndex disorder prediction False
presto_V5 ftout=T/F Make a file of UniProt features for extracted parent proteins, where possible, incoroprating SLIMs *.features.tdt
presto_V5 fullforce=T/F Force GOPHER to re-run even if alignment exists False
presto_V5 gopher=T/F Use GOPHER to generate missing orthologue alignments in alndir - see gopher.py options False
presto_V5 iupred=T/F Run IUPred disorder prediction False
presto_V5 matchic=T/F Use (and output) information content of matched regions to asses motif matches True
presto_V5 memsaver=T/F Whether to store all results in Objects (False) or clear as search proceeds (True) True
presto_V5 minimotif=T/F Input file is in minimotif format and will be reformatted (PRESTO File format only) False
presto_V5 motifaln=T/F Produce fasta files of local motif alignments False
presto_V5 motific=T/F Output Information Content for motifs False
presto_V5 motinfo=T/F Whether to output motif summary table *.motinfo.tdt None
presto_V5 msms=T/F Whether searching Tandem Mass Spec peptides False
presto_V5 mysql=T/F Output results in mySQL format - lower case headers and no spaces False
presto_V5 nohits=T/F Save list of sequence IDs without motif hits to *.nohits.txt. False
presto_V5 nrmotif=T/F Whether to remove redundancy in input motifs False
presto_V5 peptides=T/F Peptide design mode, using winsize=X to set size of peptides around motif False
presto_V5 proteinaln=T/F Search for alignments of proteins containing motifs and produce new file containing motifs False
presto_V5 ranking=T/F Whether to rank hits by their rating in MSMS mode False
presto_V5 reverse=T/F Reverse the motifs - good for generating a test comparison data set False
presto_V5 slimchg=T/F Calculate Asolute, Net and Balance charge statistics (above) for occurrences False
presto_V5 trimx=T/F Trims Xs from the ends of a motif False
presto_V5 usealn=T/F Whether to search for and use alignemnts where present. False
prodigis combcut=T/F Whether to peform combined digestions with pairs of proteases True
prodigis cyscount=T/F Whether to perform peptide count with Cysteine numbers True
prodigis cysweight=T/F Whether to weight peptide probabilities according to cysteine count True
prodigis nrpep=T/F Whether to only include the non-redundant (unique) peptides False
prodigis nterm=T/F Whether to include N-terminal peptides False
prodigis pepmwt=T/F Whether to output peptide mol weights in addition to lengths True
qslimfinder allsig=T/F Whether to also output all SLiMChance combinations (Sig/SigV/SigPrime/SigPrimeV) False
qslimfinder alphahelix=T/F Special i, i+3/4, i+7 motif discovery False
qslimfinder ambiguity=T/F (preamb=T/F) Whether to search for ambiguous motifs during motif discovery True
qslimfinder blastf=T/F Use BLAST Complexity filter when determining relationships True
qslimfinder cloudfix=T/F Restrict output to clouds with 1+ fixed motif (recommended) False
qslimfinder combamb=T/F Whether to search for combined amino acid degeneracy and variable wildcards False
qslimfinder consmask=T/F Whether to use relative conservation masking False
qslimfinder dismask=T/F Whether to mask ordered regions (see rje_disorder for options) False
qslimfinder dna=T/F Whether the sequences files are DNA rather than protein False
qslimfinder efilter=T/F Whether to use evolutionary filter True
qslimfinder force=T/F Force re-running of BLAST, UPC generation and SLiMBuild False
qslimfinder logmask=T/F Whether to log the masking of individual sequences True
qslimfinder maskfreq=T/F Whether to use masked AA Frequencies (True), or (False) mask after frequency calculations False
qslimfinder masking=T/F Master control switch to turn off all masking if False True
qslimfinder megablam=T/F Whether to create and use all-by-all GABLAM results for (gablamdis) UPC generation False
qslimfinder metmask=T/F Masks the N-terminal M (can be useful if termini=T) True
qslimfinder pickup=T/F Pick-up from aborted batch run by identifying datasets in resfile using RunID False
qslimfinder qexact=T/F Calculate exact Query motif space (True) or over-estimate from dimers (False) (quicker) True
qslimfinder seqocc=T/F Whether to upweight for multiple occurrences in same sequence (heuristic) False
qslimfinder sigprime=T/F Calculate more precise (but more computationally intensive) statistical model False
qslimfinder sigv=T/F Use the more precise (but more computationally intensive) fix to mean UPC probability False
qslimfinder slimchance=T/F Execute main QSLiMFinder probability method and outputs True
qslimfinder slimdisc=T/F Emulate SLiMDisc output format (*.rank & *.dat.rank + TEIRESIAS *.out & *.fasta) False
qslimfinder smearfreq=T/F Whether to "smear" AA frequencies across UPC rather than keep separate AAFreqs False
qslimfinder targz=T/F Whether to tar and zip dataset result files (UNIX only) False
qslimfinder teiresias=T/F Replace TEIRESIAS, making *.out and *.mask.fasta files False
qslimfinder termini=T/F Whether to add termini characters (^ & $) to search sequences True
qslimfinder wildvar=T/F Whether to allow variable length wildcards True
qslimfinder_V1.9 allsig=T/F Whether to also output all SLiMChance combinations (Sig/SigV/SigPrime/SigPrimeV) False
qslimfinder_V1.9 alphahelix=T/F Special i, i+3/4, i+7 motif discovery False
qslimfinder_V1.9 ambiguity=T/F (preamb=T/F) Whether to search for ambiguous motifs during motif discovery True
qslimfinder_V1.9 blastf=T/F Use BLAST Complexity filter when determining relationships True
qslimfinder_V1.9 cloudfix=T/F Restrict output to clouds with 1+ fixed motif (recommended) False
qslimfinder_V1.9 combamb=T/F Whether to search for combined amino acid degeneracy and variable wildcards False
qslimfinder_V1.9 consmask=T/F Whether to use relative conservation masking False
qslimfinder_V1.9 dismask=T/F Whether to mask ordered regions (see rje_disorder for options) False
qslimfinder_V1.9 dna=T/F Whether the sequences files are DNA rather than protein False
qslimfinder_V1.9 efilter=T/F Whether to use evolutionary filter True
qslimfinder_V1.9 force=T/F Force re-running of BLAST, UPC generation and SLiMBuild False
qslimfinder_V1.9 logmask=T/F Whether to log the masking of individual sequences True
qslimfinder_V1.9 maskfreq=T/F Whether to use masked AA Frequencies (True), or (False) mask after frequency calculations False
qslimfinder_V1.9 masking=T/F Master control switch to turn off all masking if False True
qslimfinder_V1.9 metmask=T/F Masks the N-terminal M (can be useful if termini=T) True
qslimfinder_V1.9 pickup=T/F Pick-up from aborted batch run by identifying datasets in resfile using RunID False
qslimfinder_V1.9 qexact=T/F Calculate exact Query motif space (True) or over-estimate from dimers (False) (quicker) True
qslimfinder_V1.9 seqocc=T/F Whether to upweight for multiple occurrences in same sequence (heuristic) False
qslimfinder_V1.9 sigprime=T/F Calculate more precise (but more computationally intensive) statistical model False
qslimfinder_V1.9 sigv=T/F Use the more precise (but more computationally intensive) fix to mean UPC probability False
qslimfinder_V1.9 slimchance=T/F Execute main QSLiMFinder probability method and outputs True
qslimfinder_V1.9 slimdisc=T/F Emulate SLiMDisc output format (*.rank & *.dat.rank + TEIRESIAS *.out & *.fasta) False
qslimfinder_V1.9 smearfreq=T/F Whether to "smear" AA frequencies across UPC rather than keep separate AAFreqs False
qslimfinder_V1.9 targz=T/F Whether to tar and zip dataset result files (UNIX only) False
qslimfinder_V1.9 teiresias=T/F Replace TEIRESIAS, making *.out and *.mask.fasta files False
qslimfinder_V1.9 termini=T/F Whether to add termini characters (^ & $) to search sequences True
qslimfinder_V1.9 wildvar=T/F Whether to allow variable length wildcards True
revert aliases=T/F Whether to use aliases in additional outputs True
revert gspcode=T/F Whether to use genome species codes for Genome field if able to parse name False
revert keepblast=T/F Whether to keep GABLAM BLAST files for reference/reuse True
revert revertnr=T/F Compile batch run results with non-redundancy and quality filtering True
revert vgablam=T/F Whether to compile viral genomes/proteomes and conduct all-by-all GABLAM for graphs True
revert vgbparse=T/F Whether to parse virus IDs from vbatch tables and output BASEFILE.HOST.acc files False
revert vspcode=T/F Whether to use viral species codes (even if invented) for VirusID aliases True
rje append=T/F Append to results files rather than overwrite False
rje backups=T/F Whether to generate backup files (True) or just overwrite without asking (False) True
rje debug=T/F Turn on additional debugging prints and prompts False
rje dev=T/F Run development-specific code. (Added to keep main coding working during dev) False
rje force=T/F Force to regenerate data rather than keep old results False
rje memsaver=T/F Some modules will have a memsaver option to save memory usage False
rje newlog=T/F Create new log file. Default = False: append log file
rje noforks=T/F Whether to avoid forks False
rje osx=T/F Run in MacOSX Mode False
rje silent=T/F If set to True will not write to screen or log. False
rje soaplab=T/F Implement special options/defaults for SoapLab implementations False
rje test=T/F Run additional testing methods and/or produce additional test outputs False
rje warn=T/F Turn on program integrity check warnings (unless silent) True
rje webserver=T/F Trigger webserver run and output False
rje win32=T/F Run in Win32 Mode False
rje_aic noutr=T/F Whether to include sequences without a 5' UTR True
rje_ancseq desconly=T/F\t Limits ancestral AAs to those found in descendants True
rje_ancseq fixdown=T/F\t Fix AAs on initial pass down tree False
rje_ancseq fixup=T/F\t Fix AAs on way up (keep probabilities) True
rje_ancseq ordered=T/F\t Order ancestral sequence output by node number False
rje_ancseq pamtree=T/F\t Calculate and output ancestral tree with PAM distances True
rje_archive checknum=T/F Whether to check numbers of files consumed by upload.sh versus directory contents True
rje_archive cleanup=T/F Whether to perform post-upload cleanup of backups and archived files True
rje_archive rmdirs=T/F Delete archived directories. (Will ask if i>0) False
rje_archive skipdormant=T/F Whether to skip uploads for dormant directories True
rje_archive skipquiet=T/F Whether to skip uploads for quiet directories True
rje_archive strict=T/F Restrict processing to projects found in Projects file and add no new ones. False
rje_archive targz=T/F Whether to tar and zip directories to be deleted True
rje_archive tryparent=T/F Whether to try to run backup parent directory in case of failure True
rje_biogrid alltypes=T/F Output a full list of PPITypes. (Will populate the PPIType list) False
rje_biogrid hostvirus=T/F Whether to pull out host-virus interactions only (MINT/IntAct only) False
rje_biogrid mitab=T/F Whether source file is in MITAB flat file format True
rje_biogrid ppifas=T/F Whether to output PPI datasets as fasta files into Species/BIOGRID_Datasets/ True
rje_biogrid ppitab=T/F Whether to output PPI table with aliases etc. True
rje_biogrid symmetry=T/F Enforce symmetry in interaction datasets True
rje_blast blastcf=T/F Use BLAST Composition-based statistics (BLAST -C X) False
rje_blast blastf=T/F Complexity Filter (BLAST -F X) True
rje_blast blastg=T/F Gapped BLAST (BLAST -g X) True
rje_blast formatdb=T/F Whether to (re)format BLAST database False
rje_blast ignoredate=T/F Ignore date stamps when deciding whether to regenerate files False
rje_blast_V1 blastcf=T/F Use BLAST Composition-based statistics (BLAST -C X) False
rje_blast_V1 blastf=T/F Complexity Filter (BLAST -F X) True
rje_blast_V1 blastg=T/F Gapped BLAST (BLAST -g X) True
rje_blast_V1 formatdb=T/F Whether to (re)format BLAST database False
rje_blast_V1 ignoredate=T/F Ignore date stamps when deciding whether to regenerate files False
rje_blast_V2 blastcf=T/F Use BLAST Composition-based statistics (BLAST -C X) False
rje_blast_V2 blastf=T/F Complexity Filter (BLAST -F X) True
rje_blast_V2 blastforce=T/F Whether to force regeneration of new BLAST results if already existing False
rje_blast_V2 blastg=T/F Gapped BLAST (BLAST -g X) True
rje_blast_V2 formatdb=T/F Whether to (re)format BLAST database False
rje_blast_V2 gzip=T/F Whether to gzip (and gunzip) BLAST results files if keeping (not Windows) True
rje_blast_V2 ignoredate=T/F Ignore date stamps when deciding whether to regenerate files False
rje_blast_V2 legacy=T/F Whether to run in "legacy" mode using old BLAST commands etc. (Currently uses BLAST) False
rje_blast_V2 oldblast=T/F Whether to run with old BLAST programs rather than new BLAST+ ones False
rje_blast_V2 qassemble=T/F Whether to fully assemble query stats from all hits False
rje_blast_V2 qassemblefas=T/F Special mode for running with outfmt=4 and then converting to fasta file False
rje_blast_V2 qcomplete=T/F Whether the query sequence should be full-length in qassemblefas output False
rje_blast_V2 runfield=T/F Whether to include Run Field in summary tables. (Useful if appending.) False
rje_blast_V2 selfsum=T/F Whether to also include self hits in qassemble output False
rje_blast_V2 softmask=T/F Whether to use soft masking for searches True
rje_conseq trimtrunc=T/F Whether to trim the leading and trailing gaps (within groups) -> change to X False
rje_db dbindex=T/F Whether to run in "index" mode, storing a file position rather than all data (read only) !Not yet implemented! False
rje_db dbindex=T/F Whether to run in "index" mode, storing a file position rather than all data (read only) !Not yet implemented! False
rje_dbase datindex=T/F Create an index file for the Uniprot DAT files in unipath if UniProt in dbprocess True
rje_dbase ensfilter=T/F Run EnsEMBL genomes through rje_seq to apply filters, rather than just concatenating False
rje_dbase ensloci=T/F Reduce EnsEMBL to a single protein per locus, mapping UniProt where possible True
rje_dbase force=T/F Whether to force regeneration of existing files False
rje_dbase formatdb=T/F Whether to BLAST format database after making True
rje_dbase ignoredate=T/F Whether to ignore the relative timestamps of files when assessing whether to regenerate False
rje_dbase inversedb=T/F TaxaList is a list of taxanomic groups *NOT* to be in database False
rje_dbase screenens=T/F Species represented by EnsEMBL will be screened out of UniProt True
rje_dbase screenipi=T/F Species represented by IPI databases will be screened out of UniProt and EnsEMBL. False
rje_dbase seqfilter=T/F Use rje_seq to filter sequences (True) or simply filter on Species Codes (False) False
rje_dbase speconly=T/F Will simply output a list of SPECIES codes to the makedb file, rather than making dbase False
rje_dbase spectable=T/F Makes a table of species codes, taxonomy and taxon_id from DAT files if dbprocess UniProt True
rje_dismatrix_V2 nsf2nwk=T/F Whether to convert extension for Newick Standard Format from nsf to nwk (for MEGA) False
rje_dismatrix_V2 symmetric=T/F Whether the matrix should be symmetrical (e.g. DisAB = DisBA) False
rje_dismatrix_V3 nsf2nwk=T/F Whether to convert extension for Newick Standard Format from nsf to nwk (for MEGA) False
rje_dismatrix_V3 symmetric=T/F Whether the matrix should be symmetrical (e.g. DisAB = DisBA) False
rje_disorder iuchdir=T/F Whether to change to IUPred directory and run (True) or rely on IUPred_PATH env variable False
rje_embl append=T/F Append to results files rather than overwrite False
rje_embl invmask=T/F Whether to invert the masking and only retain maskft features False
rje_embl makefas=T/F Generate fasta files False
rje_embl makeindex=T/F Generate UniProt index files False
rje_embl makespec=T/F Generate species table False
rje_embl memsaver=T/F Memsaver option to save memory usage - does not retain entries in object False
rje_ensembl download=T/F Download EnsEMBL databases False
rje_ensembl ensloci=T/F Create EnsEMBL datasets "reduced by loci" False
rje_ensembl enspep=T/F Create full gnspacc EnsEMBL peptide datasets False
rje_ensembl makeuniprot=T/F Whether to generate an Ensembl.dat file of UniProt entries for species False
rje_ensembl obsgo=T/F Whether to include obselete terms False
rje_ensembl speedskip=T/F Whether to assume download is fine if pep.all/cdna.all/dna.toplevel file found True
rje_ensembl splicego=T/F Whether to include all splice variants (EnsEMBL peptides) in GO datasets False
rje_forker logfork=T/F Whether to log forking in main log True
rje_forker noforks=T/F Whether to avoid forks False
rje_forker rjepy=T/F Whether forked commands are rje Python commands False
rje_genbank addtags=T/F Add locus_tag identifiers if missing - needed for gene/cds/prot fasta output False
rje_genbank locusout=T/F Whether to generate output by locus (True, locus as basefile) or combined (False) False
rje_genbank tabout=T/F Delimited table output of features False
rje_genecards fullens=T/F Incorporate all EnsLoci EnsEMBL genes into cardout file (long run!) False
rje_genecards fullhgnc=T/F Output all HGNC codes and unambiguous aliases into file False
rje_genecards purify=T/F Only output lines where the Alias and the Symbol are the same False
rje_genecards restrict=T/F Whether to only output lines for gene in the original gene=LIST False
rje_genecards update=T/F Whether to read in any data from cardout file (if present) and add to it True
rje_genecards useweb=T/F Whether to try and extract missing data from GeneCards website True
rje_genemap flatout=T/F Whether to output flatfiles (*.data.tdt & *.aliases.tdt) False
rje_genemap pickleout=T/F Whether to output pickle (*.pickle.gz) False
rje_genemap useweb=T/F Whether to try and extract missing data from GeneCards website False
rje_glossary aname=T/F Whether to hyperlink terms using a name refs True
rje_glossary href=T/F Whether to added external hyperlinks for and [text] in descriptions True
rje_glossary keeporder=T/F Keep output order the same as input order (unless terms=LIST given). Uses termsplit=X. False
rje_glossary plurals=T/F Whether to map plurals onto singular terms True
rje_go webobo=T/F Whether to download from GO website if file not given True
rje_gquad codons=T/F Perform codon/triplet analysis False
rje_gquad makeflyseq=T/F Re-annotate D.mel gene sequences with CDS and Exon positions False
rje_haq anchors=T/F Whether to use conserved 'anchors' to extend well-aligned regions in PAQ True
rje_haq manpaq=T/F Manual over-ride of sequence rejection decisions in PAQ False
rje_haq mansaq=T/F Manual over-ride of sequence rejection decisions in SAQ False
rje_hm_html fakehtml=T/F Whether to make UniFake HTML True
rje_hm_html makepng=T/F Whether to (look for and) make PNG files with R True
rje_hmm_V1 cleanres=T/F Option to reduce size of HMM results file by removing no-hit sequences True
rje_hmm_V1 force=T/F Whether to force regeneration of new HMMer results if already existing False
rje_hmm_V1 gzip=T/F Whether to gzip (and gunzip) HMMer results files (not Windows) True
rje_hmm_V1 hmmcalibrate=T/F Whether to calibrate HMM files once made True
rje_hmm_V1 hmmpfam=T/F Performs standard HMMer PFam search (--cut_ga) (or processes if present) False
rje_hmm_V2 cleanres=T/F Option to reduce size of HMM results file by removing no-hit sequences True
rje_hmm_V2 force=T/F Whether to force regeneration of new HMMer results if already existing False
rje_hmm_V2 gzip=T/F Whether to gzip (and gunzip) HMMer results files (not Windows) True
rje_hmm_V2 hmmcalibrate=T/F Whether to calibrate HMM files once made True
rje_hmm_V2 hmmpfam=T/F Performs standard HMMer PFam search (--cut_ga) (or processes if present) False
rje_hpc rjepy=T/F Whether program is an RJE *.py script (adds log processing) True
rje_hpc seqbyseq=T/F Activate seqbyseq mode - assumes basefile=X option used for output False
rje_hprd alliso=T/F Whether to include all isoforms in the output False
rje_hprd complexfas=T/F Whether to output Protein Complex fasta files False
rje_hprd domainfas=T/F Whether to output Domain fasta files False
rje_hprd genecards=T/F Make the HRPD.genecards.tdt file using rje_genecards (and its options) False
rje_hprd hprdfas=T/F Whether to generate HPRD fasta files False
rje_hprd scaled=T/F Whether distance matrix is to be scaled by total number of interactors in pairwise comparison F
rje_html nobots=T/F Whether to add code to avoid Google Bots True
rje_iridis loadbalance=T/F Whether to split SortRun jobs equally between large & small to avoid memory issues True
rje_iridis rjepy=T/F Whether program is an RJE *.py script (adds log processing) True
rje_iridis rsh=T/F Whether to use rsh to run jobs on other nodes True
rje_iridis seqbyseq=T/F Activate seqbyseq mode - assumes basefile=X option used for output False
rje_iridis sortrun=T/F Whether to sort input files by size and run big -> small to avoid hang at end True
rje_iridis test=T/F Whether to produce extra output in "test" mode False
rje_itunes addscore=T/F Adds a score of 100x Rating for each track True
rje_itunes tophtml=T/F Whether to output top tunes HTML summary True
rje_markov autoload=T/F Whether to load sequences automatically. If False, will try memory-efficient seqlist handling False
rje_markov markov=T/F Whether to perform Markov Chain Analysis of observed vs Expected for Xmers True
rje_markov scap=T/F Whether to use special SCAP sorting of xmers (sorts all but last aa) False
rje_markov sorted=T/F Whether to use sorted xmer fragments to reduce memory requirements False
rje_mascot empai=T/F Whether emPAI data is present in MASCOT file True
rje_mascot itraq=T/F Whether data is from an iTRAQ experiment False
rje_mirna seedfreq=T/F Whether to use overall Seed Frequencies per sequence for slimprob False
rje_mitab adduni=T/F Whether to add Uniprot IDs that are not returned from mapping file True
rje_mitab splicevar=T/F Whether to allow splice variants in parsed Uniprot identifiers False
rje_mitab symmetry=T/F Whether to impose hub/spoke symmetry on parsed PPI True
rje_mitab unionly=T/F Whether to restrict PPI to pairwise with UniProt IDs False
rje_motif_V3 trimx=T/F Trims Xs from the ends of a motif False
rje_motiflist consamb=T/F Whether to calculate conservation allowing for degeneracy of motif (True) or of fixed variant (False) True
rje_motiflist consinfo=T/F Weight positions by information content (does nothing for conscore=abs) True
rje_motiflist foldindex=T/F Run FoldIndex disorder prediction False
rje_motiflist ftout=T/F Make a file of UniProt features for extracted parent proteins, where possible, incoroprating SLIMs *.features.tdt
rje_motiflist gopher=T/F Use GOPHER to generate missing orthologue alignments in alndir - see gopher.py options False
rje_motiflist iupred=T/F Run IUPred disorder prediction False
rje_motiflist memsaver=T/F Whether to store all results in Objects (False) or clear as search proceeds (True) True
rje_motiflist minimotif=T/F Input file is in minimotif format and will be reformatted (PRESTO File format only) False
rje_motiflist msms=T/F Whether to include MSMS ambiguities when formatting motifs False
rje_motiflist nrmotif=T/F Whether to remove redundancy in input motifs False
rje_motiflist reverse=T/F Reverse the motifs - good for generating a test comparison data set False
rje_motiflist slimchg=T/F Calculate Asolute, Net and Balance charge statistics (above) for occurrences False
rje_motiflist trimx=T/F Trims Xs from the ends of a motif False
rje_motiflist usealn=T/F Whether to search for and use alignemnts where present. False
rje_mysql append=T/F Whether to append output files or generate new True
rje_mysql checktypes=T/F Whether to check Data Types for given file True
rje_mysql combine=T/F Whether to combine build statements in one file (True) or have separate file per table (False) True
rje_mysql header=T/F By default, the first line will be read as a header True
rje_mysql memsaver=T/F Will not check for Unique fields if True. False
rje_mysql mysql=T/F Whether to assing data types and check data (else just report lengths of field contents) True
rje_mysql subfolders=T/F Whether to look in subfolders False
rje_obj append=T/F Append to results files rather than overwrite False
rje_obj backups=T/F Whether to generate backup files (True) or just overwrite without asking (False) True
rje_obj debug=T/F Turn on additional debugging prints and prompts False
rje_obj dev=T/F Run development-specific code. (Added to keep main coding working during dev) False
rje_obj force=T/F Force to regenerate data rather than keep old results False
rje_obj memsaver=T/F Some modules will have a memsaver option to save memory usage False
rje_obj newlog=T/F Create new log file. Default = False: append log file
rje_obj noforks=T/F Whether to avoid forks False
rje_obj osx=T/F Run in MacOSX Mode False
rje_obj silent=T/F If set to True will not write to screen or log. False
rje_obj soaplab=T/F Implement special options/defaults for SoapLab implementations False
rje_obj test=T/F Run additional testing methods and/or produce additional test outputs False
rje_obj warn=T/F Turn on program integrity check warnings (unless silent) True
rje_obj webserver=T/F Trigger webserver run and output False
rje_obj win32=T/F Run in Win32 Mode False
rje_pacbio bysmrt=T/F Whether to output estimated coverage by SMRT cell rather than X coverage False
rje_pacbio calculate=T/F Calculate X coverage and target X coverage for given seed, anchor + RQ combinations False
rje_pacbio coverage=T/F Whether to generate coverage report True
rje_pacbio parameters=T/F Whether to output predicted "best" set of parameters False
rje_pacbio rqmean=T/F Whether to use mean RQ instead of min RQ for calculations False
rje_pacbio seqstats=T/F Add assembly sequence stats (if *.fas and *.preassemly.fasta files found) to parseparam run True
rje_pacbio summarise=T/F Generate subread summary statistics including ZMW summary data False
rje_paml dnds=T/F Whether to extract DN/DS results from outfile True
rje_pattern_discovery bigfirst=T/F Whether to run the biggest datasets first (e.g. for ICHEC taskfarm) True
rje_pattern_discovery memsaver=T/F Whether to run SLiMDisc in memory_saver mode (-X T) True
rje_pattern_discovery mysql=T/F MySQL mode True
rje_pattern_discovery slimdisc=T/F Whether to run list of files through SLiMDisc False
rje_pattern_discovery slimquery=T/F Whether to pull out Query Protein from name of file qry_QUERY False
rje_pattern_discovery teiresias=T/F Whether to perform TEIRESIAS search on seqin=FILE True
rje_pattern_discovery useres=T/F Whether to use existing results files or overwrite (-BT -TT) True
rje_phos filterseq=T/F Apply rje_seq sequence filters to phosphoELM data False
rje_phos phosdat=T/F Whether to produce a modified UniProt-format file with potential phosphoSites as features False
rje_phos usespec=T/F Use species codes for determing same species for ID matches True
rje_ppi colbydeg=T/F Whether to colour PNG output by node degree False
rje_ppi fragment=T/F Perform PPI fragmentation False
rje_ppi haircut=T/F Whether to perform "haircut" on MCODE complexes False
rje_ppi mcode=T/F Perform MCODE clustering False
rje_ppi multicut=T/F Whether to perform "haircut" on MCODE complexes for the purposes of looking at nodes 2+ times True
rje_ppi ppisym=T/F Whether to enforce Hub/Spoke symmetry True
rje_ppi tabout=T/F Output PPI data as Node and Edge tables False
rje_ppi xgmml=T/F Output network in XGMML style False
rje_price append=T/F Append results file if already present True
rje_price dna=T/F Whether sequences are DNA or protein True
rje_price qrygaps=T/F Whether to include gaps in the query sequence as positions to score False
rje_price weighted=T/F Weight the mean covariance by size of group True
rje_pydocs addimports=T/F Whether to add identified imported modules to python module list True
rje_pydocs calls=T/F Whether to output Method Calls False
rje_pydocs fulldoc=T/F Whether to generate full docstring output including Classes and Methods False
rje_pydocs html=T/F Whether to make a basic HTML page of module docstrings (will make linked fun later) False
rje_pydocs makepages=T/F Special run to generate default cmd/ and docs/ pages for commandline option docs False
rje_pydocs self=T/F Whether to include 'self' calls of methods if calls=T False
rje_qsub mailstart=T/F Whether to email user at start of run False
rje_qsub modpurge=T/F Whether to purge loaded modules in qsub job file prior to loading True
rje_qsub report=T/F Pull out running job IDs and run showstart False
rje_qsub rjepy=T/F Whether program is an RJE *.py script (adds python PyPath/) True
rje_samtools biallelic=T/F Whether to restrict SNPs to pure biallelic SNPs (two alleles meeting mincut) False
rje_samtools depthplot=T/F Whether to generate Xdepth plot data for the readcheck FILE. (May be slow!) False
rje_samtools ignoren=T/F Whether to exclude "N" calls from alleles True
rje_samtools ignoreref=T/F If False will always keep Reference allele and call fixed change as SNP False
rje_samtools indels=T/F Whether to include indels in "SNP" parsing True
rje_samtools majdif=T/F Whether to restrict output and stats to positions with Major Allele differences in sample False
rje_samtools majfocus=T/F Whether the focus is on Major Alleles (True) or Mutant/Reference Alleles (False) True
rje_samtools majmut=T/F Whether to restrict output and stats to positions with non-reference Major Allele True
rje_samtools majref=T/F Whether to restrict output and stats to positions with reference Major Allele (if majmut=F) False
rje_samtools readlen=T/F Include read length data for the readcheck file (if depthplot=T) True
rje_samtools rgraphics=T/F Whether to generate PNG graphics using R. (Needs R installed and setup) True
rje_samtools rid=T/F Whether to include Read ID (number) lists for each allele True
rje_samtools snponly=T/F Whether to restrict parsing output to SNP positions (will use mincut settings below) False
rje_samtools snptableout=T/F Output filtered alleles to SNP Table False
rje_samtools_V0 ignoren=T/F Whether to exclude "N" calls for major/minor alleles True
rje_samtools_V0 majdif=T/F Whether to restrict output and stats to positions with Major Allele differences True
rje_samtools_V0 majmut=T/F Whether to restrict output and stats to positions with non-reference Major Allele False
rje_seq accnr=T/F Check for redundant Accession Numbers/Names on loading sequences. True
rje_seq align=T/F Whether the sequences should be aligned. Will align if unaligned. False
rje_seq autofilter=T/F Whether to automatically apply sequence filters etc. upon loading sequence True
rje_seq autoload=T/F Whether to automatically load sequences upon initiating object True
rje_seq countspec=T/F Generate counts of different species and output in log False
rje_seq dbonly=T/F Whether to only allow sequences from listed databases False
rje_seq degap=T/F Degaps each sequence False
rje_seq dna=T/F Alternative identification of sequences as DNA False
rje_seq gapfilter=T/F Whether to filter gappy sequences upon loading True
rje_seq gnspacc=T/F Convert sequence names into gene_SPECIES__AccNum format wherever possible. False
rje_seq keepblast=T/F Whether to keep BLAST results files for blast2fas searches True
rje_seq logrem=T/F Whether to log removed sequences True
rje_seq makepng=T/F Whether to make RelCons PNG files False
rje_seq memsaver=T/F Minimise memory usage. Input sequences must be fasta. False
rje_seq mixed=T/F Whether to allow auto-identification of mixed sequences types (else uses first seq only) False
rje_seq nosplice=T/F If nosplice=T, UniProt splice variants will be filtered out False
rje_seq nralign=T/F Use ALIGN for non-redundancy calculations rather than GABLAMO False
rje_seq nrkeepann=T/F Append annotation of redundant sequences onto NR sequences False
rje_seq querynr=T/F Perform Non-Redundancy on Query species (True) or limit to non-Query species (False) True
rje_seq replacechar=T/F Whether to remove numbers and replace characters not found in the given alphabet with 'X' True
rje_seq rna2dna=T/F Converts RNA to DNA False
rje_seq seqnr=T/F Make sequences Non-Redundant False
rje_seq specnr=T/F Non-Redundancy within same species only False
rje_seq tidygap=T/F Removes any columns from alignments that are 100% gap True
rje_seq unkspec=T/F Whether sequences of unknown species are allowed True
rje_seq usecase=T/F Whether to output sequences in mixed case rather than converting all to upper case False
rje_seq win32=T/F Run in Win32 Mode False
rje_seqgen append=T/F Whether to append to outfile False
rje_seqgen blastgen=T/F Activate the BLASTGen method False
rje_seqgen estgen=T/F Whether to run EST randomiser method False
rje_seqgen fullscramble=T/F Generate all possible scrambles for each peptide in TDT False
rje_seqgen keepnames=T/F Whether to keep same input names in outfile False
rje_seqgen nrgen=T/F Whether to generate a non-redundant sequence list (whole-sequence redundancies only) True
rje_seqgen poolgen=T/F Whether to build sequences using a fixed AA pool (exact freqs) or probabilities only False
rje_seqgen randdesc=T/F Whether to include construction details in description line of output file True
rje_seqgen scramble=T/F Run peptide scrambler False
rje_seqgen screenrev=T/F Whether to screen reverse Xmers too False
rje_seqgen xmerocc=T/F Whether to output occurrences of screened Xmers True
rje_seqlist autofilter=T/F Whether to automatically apply sequence filtering. True
rje_seqlist autoload=T/F Whether to automatically load sequences upon initialisation. True
rje_seqlist concatenate=T Concenate sequences into single output sequence named after file False
rje_seqlist dna=T/F Alternative option to indicate dealing with nucleotide sequences False
rje_seqlist mixed=T/F Whether to allow auto-identification of mixed sequences types (else uses first seq only) False
rje_seqlist orfmet=T/F Whether ORFs must start with a methionine (before minorf cutoff) True
rje_seqlist rename=T/F Whether to rename sequences False
rje_seqlist revcompnr=T/F Whether to check reverse complement for redundancy too False
rje_seqlist seqindex=T/F Whether to save (and load) sequence index file in file mode. True
rje_seqlist seqnr=T/F Whether to check for redundancy on loading. (Will remove, save and reload if found) False
rje_seqlist seqshuffle=T/F Randomly shuffle each sequence without replacement (maintains monomer composition) False
rje_seqlist summarise=T/F Generate some summary statistics in log file for sequence data after loading False
rje_seqlist usecase=T/F Whether to return sequences in the same case as input (True), or convert to Upper (False) False
rje_seqplot occonly=T/F Only output sequences with motif occurrences False
rje_seqplot rescale=T/F Whether to rescale plotstats (Truncate at 0.0 and normalise to max 1.0) True
rje_sleeper tofile=T/F Whether to print to file True
rje_sleeper toscreen=T/F Whether to print to file False
rje_slim dna=T/F Whether motifs should be considered as DNA motifs False
rje_slim trimx=T/F Trims Xs from the ends of a motif False
rje_slimcalc consamb=T/F Whether to calculate conservation allowing for degeneracy of motif (True) or of fixed variant (False) True
rje_slimcalc consinfo=T/F Weight positions by information content (does nothing for conscore=abs) True
rje_slimcalc fullforce=T/F Whether to force regeneration of alignments using GOPHER False
rje_slimcalc homfilter=T/F Whether to filter homologues using seqfilter options False
rje_slimcalc masking=T/F Whether to use seq.info['MaskSeq'] for Prob cons, if present (else 'Sequence') True
rje_slimcalc relgappen=T/F Whether to invoke the "Gap Penalty" during relative conservation calculations True
rje_slimcalc usealn=T/F Whether to search for and use alignments where present. False
rje_slimcalc usegopher=T/F Use GOPHER to generate orthologue alignments missing from alndir - see gopher.py options False
rje_slimcore blastf=T/F Use BLAST Complexity filter when determining relationships True
rje_slimcore consmask=T/F Whether to use relative conservation masking False
rje_slimcore dismask=T/F Whether to mask ordered regions (see rje_disorder for options) False
rje_slimcore dna=T/F Whether the sequences files are DNA rather than protein False
rje_slimcore efilter=T/F Whether to use evolutionary filter True
rje_slimcore extras=T/F Whether to generate additional output files (distance matrices etc.) True
rje_slimcore fakemask=T/F Whether to invoke UniFake to generate additional features for masking False
rje_slimcore force=T/F Force re-running of BLAST, UPC generation and SLiMBuild False
rje_slimcore fupc=T/F Whether to use experimental "Fragment UPC" approach for UPC of large proteomes False
rje_slimcore logmask=T/F Whether to output the log messages for masking of individual sequences to screen False
rje_slimcore maskfreq=T/F Whether to use masked AA Frequencies (True), or (False) mask after frequency calculations True
rje_slimcore masking=T/F Master control switch to turn off all masking if False True
rje_slimcore maskpickle=T/F Whether to save/load pickle of masked input data, independent of main pickling False
rje_slimcore megablam=T/F Whether to create and use all-by-all GABLAM results for (gablamdis) UPC generation False
rje_slimcore megaslimfix=T/F Whether to run megaslim in "fix" mode to tidy/repair existing files False
rje_slimcore metmask=T/F Masks the N-terminal M (can be useful if SLiMFinder termini=T) *Also maskm=T/F* True
rje_slimcore pickle=T/F Whether to save/use pickles True
rje_slimcore protscores=T/F Whether to save individual protein rlc.txt files in alignment directory False
rje_slimcore randomise=T/F Randomise UPC within batch files and output new datasets False
rje_slimcore slimbuild=T/F Whether to build motifs with SLiMBuild. (For combination with motifseq only.) True
rje_slimcore smearfreq=T/F Whether to "smear" AA frequencies across UPC rather than keep separate AAFreqs False
rje_slimcore targz=T/F Whether to tar and zip dataset result files (UNIX only) False
rje_slimfungo webobo=T/F Whether to download from GO website if file not given True
rje_slimhtml addrand=T/F Whether to add pages for random data True
rje_slimhtml fakehtml=T/F Whether to make UniFake HTML True
rje_slimhtml makepng=T/F Whether to (look for and) make PNG files with R True
rje_slimhtml pround=T/F Whether to round off occurrence positions for PNGs True
rje_slimhtml svg=T/F Make SVG files rather than PNG files True
rje_slimlist dna=T/F Whether motifs should be considered as DNA motifs False
rje_slimlist ftout=T/F Make a file of UniProt features for extracted parent proteins, where possible, incoroprating SLIMs *.features.tdt
rje_slimlist gopher=T/F Use GOPHER to generate missing orthologue alignments in alndir - see gopher.py options False
rje_slimlist minimotif=T/F Input file is in minimotif format and will be reformatted (PRESTO File format only) False
rje_slimlist nrmotif=T/F Whether to remove redundancy in input motifs False
rje_slimlist peptides=T/F Whether to output peptide sequences based on motif and winsize False
rje_slimlist reverse=T/F Reverse the motifs - good for generating a test comparison data set False
rje_slimlist trimx=T/F Trims Xs from the ends of a motif False
rje_slimlist usealn=T/F Whether to search for and use alignemnts where present. False
rje_slimlist varlength=T/F Whether to motifs can have flexible-length elements True
rje_slimlist wildscram=T/F Perform a wildcard spacer scrambling - good for generating a test comparison data set False
rje_synteny proteins=T/F Whether input is protein sequences (True) or genes (False) False
rje_taxamap bootweight=T/F Whether to weight taxon scores for each protein by clade bootstrap support for filtering True
rje_taxamap monophyly=T/F Enforce strict monophyly and change any multiple assignments to "Uncertain" False
rje_taxonomy batchmode=T/F Treat each element of taxin as a separate run (will be used for output basefile) False
rje_taxonomy download=T/F Whether to download files directly from websites where possible if missing True
rje_taxonomy nodeonly=T/F Whether to limit output to the matched nodes (i.e. no children) False
rje_taxonomy rankonly=T/F Whether to limit output to species-level taxonomic codes False
rje_tm maskcleave=T/F Whether to output sequences with cleaved signal peptides masked. False
rje_tm mysql=T/F Output results in tdt files for mySQL import True
rje_tree allowvar=T/F Allow variants of same species within a group. False
rje_tree autoload=T/F Whether to automatically load sequences upon initiating object True
rje_tree branchlen=T/F Whether to use branch lengths in output tree True
rje_tree kimura=T/F Whether to use Kimura correction for multiple hits True
rje_tree orphan=T/F Whether orphans sequences (not in subfam) allowed. True
rje_tree qryvar=T/F Keep variants of query species within a group (over-rides allowvar=F). False
rje_tree seqnum=T/F Output sequence numbers (if making tree from sequences) True
rje_uniprot append=T/F Append to results files rather than overwrite False
rje_uniprot cc2ft=T/F Extra whole-length features added for TISSUE and LOCATION (not in datout) False
rje_uniprot cleardata=T/F Whether to clear unprocessed Entry data (True) or (False) retain in Entry & Sequence objects True
rje_uniprot complete=T/F Whether to restrict proteome downloads to "complete proteome" sets False
rje_uniprot dbdetails=T/F Whether to extract full details of DR line rather than parsing DB xref only False
rje_uniprot dbsplit=T/F Whether to generate a table per dblist database (basefile.dbase.tdt) False
rje_uniprot domtable=T/F Makes a table of domains from uniprot file False
rje_uniprot fullref=T/F Whether to store full Reference information in UniProt Entry objects False
rje_uniprot gotable=T/F Makes a table of AccNum:GO mapping False
rje_uniprot grepdat=T/F Whether to use GREP in attempt to speed up processing False
rje_uniprot invmask=T/F Whether to invert the masking and only retain maskft features False
rje_uniprot longlink=T/F Whether link table is to be "long" (acc,db,dbacc) or "wide" (acc, dblinks) True
rje_uniprot makefas=T/F Generate fasta files False
rje_uniprot makeindex=T/F Generate UniProt index files False
rje_uniprot makespec=T/F Generate species table False
rje_uniprot memsaver=T/F Memsaver option to save memory usage - does not retain entries in UniProt object False
rje_uniprot reviewed=T/F Whether to restrict input to reviewed entries only False
rje_uniprot splicevar=T/F Whether to search for AccNum allowing for splice variants (AccNum-X) True
rje_uniprot tmconvert=T/F Whether to convert TOPO_DOM features, using first description word as Type False
rje_uniprot usebeta=T/F Whether to use beta.uniprot.org rather than www.uniprot.org False
rje_xref fullmap=T/F Whether to map onto ALL map fields or stop at first hit False
rje_xref maptomany=T/F Whether to keep potential one-to-many mapfield IDs True
rje_xref naturaljoin=T/F Whether to only output entries that join to all tables False
rje_xref onetomany=T/F Whether to keep potential one-to-many altkeys IDs False
rje_xref savexref=T/F Save the xrefdata table (*.xref.tdt) following compilation of data True
rje_xref sortxref=T/F Whether to sort multiple xref data alphabetically True
rje_xref splitcsv=T/F Whether to also split fields based on comma separation True
rje_xref uniquexref=T/F Whether to restrict analysis to unique XRef IDs False
rje_xref xreformat=T/F Whether to apply field reformatting to input xrefdata (True) or just xrefs to map (False) False
rje_yeast gopher=T/F Whether to feed Pillars into GOPHER Orthology (at BLAST ID stage) False
rje_yeast sgd2sp=T/F Convert SGD identifiers into SwissProt identifiers False
samphaser halfhap=T/F Whether to allow "half haplotigs" where one halpotig in a pair is removed by minhapx True
samphaser indels=T/F Whether to include indels in "SNP" parsing True
samphaser phaseindels=T/F Whether to include indels in "SNP" phasing False
samphaser rgraphics=T/F Whether to generate PNG graphics using R. (Needs R installed and setup) True
samphaser snptableout=T/F Output filtered alleles to SNP Table False
scap sorted=T/F Whether to use sorted xmer fragments to reduce memory requirements False
seqforker append=T/F Will append to results files rather than overwrite False
seqforker newlog=T/F Create new log file. Default = False: append log file
seqforker noforks=T/F Whether to avoid forks False
seqmapper append=T/F Append rather than overwrite results files False
seqmapper blastf=T/F Complexity Filter (BLAST -F X) False
seqmapper combine=T/F Combine both fasta files in one (e.g. include unmapped sequences in *.mapping.fas) False
seqmapper gablamout=T/F Output GABLAM statistics for mapped sequences, including "straight" matches True
seqmapper ordered=T/F Whether to use GABLAMO rather than GABLAM stat True
seqsuite batchbase=T/F Whether to give each batch run a separate basefile=X command in place of log=X True
seqsuite help=T/F Show the help documentation for program X. False
slim_pickings abschg=T/F Whether to output number of charged positions (KRDE) True
slim_pickings advprob=T/F Calculate advanced probability based on actual sequences containing motifs False
slim_pickings ailmv=T/F Whether to output if all positions in the motif are A,I,L,M or V. True
slim_pickings append=T/F Append file rather than over-writing False
slim_pickings aromatic=T/F Whether to output count of F+Y+W True
slim_pickings balchg=T/F Whether to output the *balance* of charge (netNT - netCT) True
slim_pickings bigindex=T/F Whether to use the special makeBigIndexFiles() method False
slim_pickings compile=T/F Compile motifs from SliMDisc rank files into output file. (False=index only) True
slim_pickings expect=T/F Calculate min. expected occurrence of motif in search dataset True
slim_pickings extract=T/F Extract additional data for motifs True if datasets/SLiMs/accnums given, else False
slim_pickings fullpath=T/F Whether to use full path (else relative) for dataset index True
slim_pickings gopher=T/F Use GOPHER to generate missing orthologue alignments in alndir - see gopher.py options False
slim_pickings index=T/F Whether to create index files (slimpicks.*.index) for proteins, motifs and datasets True
slim_pickings lencorrect=T/F Implements crude length correction in RScore False
slim_pickings motifaln=T/F Produce fasta files of local motif alignments True
slim_pickings motific=T/F Recalulate IC using PRESTO. Used for re-ranking. OldIC also output. False
slim_pickings netchg=T/F Whether to output net charge of motif (KR) - (DE) True
slim_pickings peptides=T/F Peptide design around discovered motifs False
slim_pickings phos=T/F Whether to output potential phosphorylated residues X (none) or [S][T][Y], if present True
slim_pickings proteinaln=T/F Search for alignments of proteins containing motifs and produce new file containing motifs True
slim_pickings rankfilter=T/F Re-ranks the filtered dataset (True) rather than the whole (pre-filtered) dataset (False) True
slim_pickings slimchg=T/F Calculate selected charge statistics (above) for occurrences in addition to pattern False
slim_pickings slimcons=T/F Calculate Conservation stats for SLiMDisc results False
slim_pickings slimfold=T/F Calculate disorder using FoldIndex over the internet False
slim_pickings slimhyd=T/F Calculate Eisenbeg Hydophobicity for SLiMDisc Results True
slim_pickings slimiup=T/F Calculate disorder using local IUPred True
slim_pickings slimsa=T/F Calculate SA information for SLiMDisc Results True
slim_pickings strict=T/F Only extract protein/occurrence details for those proteins in protlist False
slim_pickings subdir=T/F Whether to search subdirectories for rank files True
slim_pickings unitab=T/F Make tables of UniProt data using rje_uniprot.py True
slim_pickings zfilter=T/F Calculate the Z-score on the filtered dataset (True) or the whole dataset (False) False
slim_pickings zscore=T/F Calculate z-scores for each motif using the entire dataset (<=slimranks) True
slimbench backups=T/F Whether to (prompt if interactive and) generate backups before overwriting files True
slimbench balanced=T/F Whether to reduce benchmarking to datasets found for all RunIDs True
slimbench benchmark=T/F Whether to perfrom SLiMBench benchmarking assessment against motif file False
slimbench dombench=T/F Whether to generate Pfam domain ELM PPI datasets True
slimbench domlink=T/F Link ELMs to PPI via Pfam domains (True) or (False) just use direct protein links True
slimbench download=T/F Whether to download files directly from websites where possible if missing True
slimbench elmbench=T/F Whether to generate ELM datasets True
slimbench force=T/F Whether to force regeneration of outputs (True) or assume existing outputs are right False
slimbench generate=T/F Whether to generate SLiMBench datasets from ELM input. False
slimbench integrity=T/F Whether to quit by default if source data integrity is breached False
slimbench masking=T/F Whether to use SLiMCore masking for query selection True
slimbench noamb=T/F Filter out ambiguous patterns False
slimbench occbench=T/F Whether to generate ELM OccBench datasets True
slimbench ppibench=T/F Whether to generate ELM PPI datasets True
slimbench queries=T/F Whether to datasets have specific Query proteins False
slimbench ranbench=T/F Whether to generate randomised datasets (part of simulation if simbench=T) False
slimbench randat=T/F Whether to use DAT file for random source False
slimbench simbench=T/F Whether to generate simulated datasets using reduced ELMs (if found) False
slimbench slimmaker=T/F Whether to use SLiMMaker to "reduce" ELMs to more findable SLiMs True
slimbench_V1 backups=T/F Whether to (prompt if interactive and) generate backups before overwriting files True
slimbench_V1 benchmark=T/F Whether to perfrom SLiMBench benchmarking assessment against motif file False
slimbench_V1 force=T/F Whether to force regeneration of outputs (True) or assume existing outputs are right False
slimbench_V1 generate=T/F Whether to generate SLiMBench datasets from ELM input False
slimbench_V1 integrity=T/F Whether to quit by default if input integrity is breached True
slimbench_V1 masking=T/F Whether to use SLiMCore masking for query selection True
slimbench_V1 noamb=T/F Filter out ambiguous patterns False
slimbench_V1 queries=T/F Whether to generate datasets with specific Query proteins True
slimbench_V1 randomise=T/F Whether to generate randomised datasets (part of simulation if simulate=T) False
slimbench_V1 simulate=T/F Whether to generate simulated datasets using reduced ELMs (if found) False
slimbench_V1 slimmaker=T/F Whether to use SLiMMaker to "reduce" ELMs to more findable SLiMs True
slimfarmer loadbalance=T/F Whether to split SortRun jobs equally between large & small to avoid memory issues True
slimfarmer mailstart=T/F Whether to email user at start of run False
slimfarmer modpurge=T/F Whether to purge loaded modules in qsub job file prior to loading True
slimfarmer pickup=T/F Whether to pickup previous run based on existing results and RunID True
slimfarmer qsub=T/F Whether to execute QSub PDB job creation and queuing False
slimfarmer report=T/F Pull out running job IDs and run showstart False
slimfarmer seqbyseq=T/F Activate seqbyseq mode - assumes basefile=X option used for output False
slimfarmer slimsuite=T/F Whether program is an RJE *.py script (adds log processing) True
slimfarmer sortrun=T/F Whether to sort input files by size and run big -> small to avoid hang at end True
slimfarmer test=T/F Whether to produce extra output in "test" mode False
slimfinder allsig=T/F Whether to also output all SLiMChance combinations (Sig/SigV/SigPrime/SigPrimeV) False
slimfinder alphahelix=T/F Special i, i+3/4, i+7 motif discovery False
slimfinder ambiguity=T/F (preamb=T/F) Whether to search for ambiguous motifs during motif discovery True
slimfinder blastf=T/F Use BLAST Complexity filter when determining relationships True
slimfinder cloudfix=T/F Restrict output to clouds with 1+ fixed motif (recommended) False
slimfinder combamb=T/F Whether to search for combined amino acid degeneracy and variable wildcards False
slimfinder consmask=T/F Whether to use relative conservation masking False
slimfinder dimfreq=T/F Whether to use dimer masking pattern to adjust number of possible sites for motif True
slimfinder dismask=T/F Whether to mask ordered regions (see rje_disorder for options) False
slimfinder dna=T/F Whether the sequences files are DNA rather than protein False
slimfinder efilter=T/F Whether to use evolutionary filter True
slimfinder fixlen=T/F If true, will use maxwild and slimlen to define a fixed total motif length False
slimfinder force=T/F Force re-running of BLAST, UPC generation and SLiMBuild False
slimfinder logmask=T/F Whether to log the masking of individual sequences True
slimfinder maskfreq=T/F Whether to use masked AA Frequencies (True), or (False) mask after frequency calculations True
slimfinder masking=T/F Master control switch to turn off all masking if False True
slimfinder megablam=T/F Whether to create and use all-by-all GABLAM results for (gablamdis) UPC generation False
slimfinder metmask=T/F Masks the N-terminal M (can be useful if termini=T) True
slimfinder oldscores=T/F Whether to also output old SLiMDisc score (S) and SLiMPickings score (R) False
slimfinder palindrome=T/F Special DNA mode that will search for palindromic sequences only False
slimfinder pickall=T/F Whether to skip aborted runs (True) or only those datasets that ran to completion (False) True
slimfinder pickid=T/F Whether to use RunID to identify run datasets when using pickup True
slimfinder pickup=T/F Pick-up from aborted batch run by identifying datasets in resfile False
slimfinder randomise=T/F Randomise UPC within batch files and output new datasets False
slimfinder seqocc=T/F Whether to upweight for multiple occurrences in same sequence (heuristic) False
slimfinder sigprime=T/F Calculate more precise (but more computationally intensive) statistical model False
slimfinder sigv=T/F Use the more precise (but more computationally intensive) fix to mean UPC probability False
slimfinder slimbuild=T/F Whether to build motifs with SLiMBuild. (For combination with motifseq only.) True
slimfinder slimchance=T/F Execute main SLiMFinder probability method and outputs True
slimfinder slimdisc=T/F Emulate SLiMDisc output format (*.rank & *.dat.rank + TEIRESIAS *.out & *.fasta) False
slimfinder smearfreq=T/F Whether to "smear" AA frequencies across UPC rather than keep separate AAFreqs False
slimfinder targz=T/F Whether to tar and zip dataset result files (UNIX only) False
slimfinder teiresias=T/F Replace TEIRESIAS, making *.out and *.mask.fasta files False
slimfinder termini=T/F Whether to add termini characters (^ & $) to search sequences True
slimfinder wildvar=T/F Whether to allow variable length wildcards True
slimfinder_V4.9 allsig=T/F Whether to also output all SLiMChance combinations (Sig/SigV/SigPrime/SigPrimeV) False
slimfinder_V4.9 alphahelix=T/F Special i, i+3/4, i+7 motif discovery False
slimfinder_V4.9 ambiguity=T/F (preamb=T/F) Whether to search for ambiguous motifs during motif discovery True
slimfinder_V4.9 blastf=T/F Use BLAST Complexity filter when determining relationships True
slimfinder_V4.9 cloudfix=T/F Restrict output to clouds with 1+ fixed motif (recommended) False
slimfinder_V4.9 combamb=T/F Whether to search for combined amino acid degeneracy and variable wildcards False
slimfinder_V4.9 consmask=T/F Whether to use relative conservation masking False
slimfinder_V4.9 dimfreq=T/F Whether to use dimer masking pattern to adjust number of possible sites for motif True
slimfinder_V4.9 dismask=T/F Whether to mask ordered regions (see rje_disorder for options) False
slimfinder_V4.9 dna=T/F Whether the sequences files are DNA rather than protein False
slimfinder_V4.9 efilter=T/F Whether to use evolutionary filter True
slimfinder_V4.9 fixlen=T/F If true, will use maxwild and slimlen to define a fixed total motif length False
slimfinder_V4.9 force=T/F Force re-running of BLAST, UPC generation and SLiMBuild False
slimfinder_V4.9 logmask=T/F Whether to log the masking of individual sequences True
slimfinder_V4.9 maskfreq=T/F Whether to use masked AA Frequencies (True), or (False) mask after frequency calculations True
slimfinder_V4.9 masking=T/F Master control switch to turn off all masking if False True
slimfinder_V4.9 metmask=T/F Masks the N-terminal M (can be useful if termini=T) True
slimfinder_V4.9 oldscores=T/F Whether to also output old SLiMDisc score (S) and SLiMPickings score (R) False
slimfinder_V4.9 palindrome=T/F Special DNA mode that will search for palindromic sequences only False
slimfinder_V4.9 pickall=T/F Whether to skip aborted runs (True) or only those datasets that ran to completion (False) True
slimfinder_V4.9 pickid=T/F Whether to use RunID to identify run datasets when using pickup True
slimfinder_V4.9 pickup=T/F Pick-up from aborted batch run by identifying datasets in resfile False
slimfinder_V4.9 randomise=T/F Randomise UPC within batch files and output new datasets False
slimfinder_V4.9 seqocc=T/F Whether to upweight for multiple occurrences in same sequence (heuristic) False
slimfinder_V4.9 sigprime=T/F Calculate more precise (but more computationally intensive) statistical model False
slimfinder_V4.9 sigv=T/F Use the more precise (but more computationally intensive) fix to mean UPC probability False
slimfinder_V4.9 slimbuild=T/F Whether to build motifs with SLiMBuild. (For combination with motifseq only.) True
slimfinder_V4.9 slimchance=T/F Execute main SLiMFinder probability method and outputs True
slimfinder_V4.9 slimdisc=T/F Emulate SLiMDisc output format (*.rank & *.dat.rank + TEIRESIAS *.out & *.fasta) False
slimfinder_V4.9 smearfreq=T/F Whether to "smear" AA frequencies across UPC rather than keep separate AAFreqs False
slimfinder_V4.9 targz=T/F Whether to tar and zip dataset result files (UNIX only) False
slimfinder_V4.9 teiresias=T/F Replace TEIRESIAS, making *.out and *.mask.fasta files False
slimfinder_V4.9 termini=T/F Whether to add termini characters (^ & $) to search sequences True
slimfinder_V4.9 wildvar=T/F Whether to allow variable length wildcards True
slimfrap annotate=T/F Whether to manually annotate/classify SLiMs False
slimfrap frapout=T/F Whether to generate SLiMFRAP 0.0 output tables False
slimfrap skipknown=T/F Whether to skip known SLiMs in manual annotation (True), or ask to check (False) False
slimfrap slimjim=T/F Whether to process data for SLiMJIM output True
slimfrap usego=T/F Whether to use GO datasets False
slimfrap usenandr=T/F Whether to use Neduva & Russell results False
slimjim domains=T/F Whether to generate output for Domains True
slimjim htmlall=T/F Whether to make HTML for all datasets or only those identified with hublist False
slimjim hubs=T/F Whether to generate output for Hubs True
slimjim iridis=T/F Whether running on IRIDIS - fork out R jobs False
slimjim mains=T/F Whether to generate main analysis pages True
slimjim makehtml=T/F Whether to generate linked HTML output files False
slimjim makejim=T/F Whether to generate data and PNG files False
slimjim motifs=T/F Whether to generate output for Motifs True
slimjim spokes=T/F Whether to generate output for Spokes True
slimjim tableonly=T/F Only make delimited text versions of tables, not all HTML files False
slimjim unihtml=T/F Generate missing linked HTML DAT files True
slimmaker dna=T/F Whether "peptides" are actually DNA fragments False
slimmaker extendaa=T/F Whether to extend ambiguous aa using equivalence list False
slimmaker iterate=T/F Whether to perform iterative SLiMMaker, re-running on matched peptides with each iteration False
slimmaker varlength=T/F Whether to identifies gaps in aligned peptides and generate variable length motif True
slimmutant analyse=T/F Whether to analyse the results of a SLiMProb run False
slimmutant generate=T/F Whether to run sequence generation pipeline False
slimmutant slimppi=T/F Whether to perform SLiMPPI analysis (will set analyse=T) False
slimmutant slimprob=T/F Whether to run SLiMProb on *.wildtype.fas and *.mutant.fas (*=basefile) False
slimparser pureapi=T/F Whether to return the text returned from the REST call. Needs rest=X. False
slimparser restout=T/F Whether to save extracted elements to individual files False
slimprob blastf=T/F Use BLAST Complexity filter when determining relationships True
slimprob consmask=T/F Whether to use relative conservation masking False
slimprob dismask=T/F Whether to mask ordered regions (see rje_disorder for options) False
slimprob dna=T/F Whether the sequences files are DNA rather than protein False
slimprob efilter=T/F Whether to use evolutionary filter True
slimprob force=T/F Force re-running of BLAST, UPC generation and search False
slimprob maskfreq=T/F Whether to use masked AA Frequencies (True), or (False) mask after frequency calculations True
slimprob masking=T/F Master control switch to turn off all masking if False False
slimprob megablam=T/F Whether to create and use all-by-all GABLAM results for (gablamdis) UPC generation False
slimprob mergesplits=T/F Whether to merge split SLiMs for recalculating statistics. (Assumes unique RunIDs) True
slimprob metmask=T/F Masks the N-terminal M False
slimprob occupc=T/F Whether to output the UPC ID number in the occurrence output file False
slimprob pickle=T/F Whether to save/use pickles True
slimprob smearfreq=T/F Whether to "smear" AA frequencies across UPC rather than keep separate AAFreqs False
slimprob targz=T/F Whether to tar and zip dataset result files (UNIX only) False
slimprob_V1.4 blastf=T/F Use BLAST Complexity filter when determining relationships True
slimprob_V1.4 consmask=T/F Whether to use relative conservation masking False
slimprob_V1.4 dismask=T/F Whether to mask ordered regions (see rje_disorder for options) False
slimprob_V1.4 efilter=T/F Whether to use evolutionary filter False
slimprob_V1.4 force=T/F Force re-running of BLAST, UPC generation and search False
slimprob_V1.4 maskfreq=T/F Whether to use masked AA Frequencies (True), or (False) mask after frequency calculations True
slimprob_V1.4 masking=T/F Master control switch to turn off all masking if False False
slimprob_V1.4 metmask=T/F Masks the N-terminal M False
slimprob_V1.4 occupc=T/F Whether to output the UPC ID number in the occurrence output file False
slimprob_V1.4 pickle=T/F Whether to save/use pickles True
slimprob_V1.4 smearfreq=T/F Whether to "smear" AA frequencies across UPC rather than keep separate AAFreqs False
slimprob_V1.4 targz=T/F Whether to tar and zip dataset result files (UNIX only) False
slimsearch blastf=T/F Use BLAST Complexity filter when determining relationships True
slimsearch consmask=T/F Whether to use relative conservation masking False
slimsearch dismask=T/F Whether to mask ordered regions (see rje_disorder for options) False
slimsearch efilter=T/F Whether to use evolutionary filter False
slimsearch force=T/F Force re-running of BLAST, UPC generation and search False
slimsearch maskfreq=T/F Whether to use masked AA Frequencies (True), or (False) mask after frequency calculations True
slimsearch masking=T/F Master control switch to turn off all masking if False False
slimsearch metmask=T/F Masks the N-terminal M False
slimsearch occupc=T/F Whether to output the UPC ID number in the occurrence output file False
slimsearch pickle=T/F Whether to save/use pickles True
slimsearch smearfreq=T/F Whether to "smear" AA frequencies across UPC rather than keep separate AAFreqs False
slimsearch targz=T/F Whether to tar and zip dataset result files (UNIX only) False
slimsuite help=T/F Return the help documentation for program X. False
smrtscape bysmrt=T/F Whether to output estimated coverage by SMRT cell rather than X coverage False
smrtscape calculate=T/F Calculate X coverage and target X coverage for given seed, anchor + RQ combinations False
smrtscape coverage=T/F Whether to generate coverage report False
smrtscape force=T/F [Adv.] Whether to force regeneration of existing data, except `unique` and `zmw` tables False
smrtscape fullforce=T/F [Adv.] Whether to force regeneration of existing data including `unique` and `zmw` tables False
smrtscape optimise=T/F Whether to output predicted "best" set of optimised parameters False
smrtscape summarise=T/F Generate subread summary statistics including ZMW summary data False
smrtscape_V1 bysmrt=T/F Whether to output estimated coverage by SMRT cell rather than X coverage False
smrtscape_V1 calculate=T/F Calculate X coverage and target X coverage for given seed, anchor + RQ combinations False
smrtscape_V1 coverage=T/F Whether to generate coverage report False
smrtscape_V1 parameters=T/F Whether to output predicted "best" set of parameters False
smrtscape_V1 predict=T/F Whether to add XCoverage prediction and efficiency estimation from parameters and subreads False
smrtscape_V1 summarise=T/F Generate subread summary statistics including ZMW summary data False
snapper altft=T/F Use AltLocus and AltPos for feature mapping (if altpos=T) False
snapper altpos=T/F Whether SNP file is a single mapping (with AltPos) (False=BCF) True
snapper filterself=T/F Filter out self-hits prior to Snapper pipeline (e.g for assembly all-by-all) False
snapper localsAM=T/F Save local (and unique) hits data as SAM files in addition to TDT False
snapper makesnp=T/F Whether or not to generate Query vs Reference SNP tables True
snapper nocopyfas=T/F Whether to output CNV=0 fragments to *.nocopy.fas fasta file True
snp_mapper altft=T/F Use AltLocus and AltPos for feature mapping (if altpos=T) False
snp_mapper altpos=T/F Whether SNP file is a single mapping (with AltPos) (False=BCF) True
snp_mapper snpbyftype=T/F Whether to output mapped SNPs by feature type (before FTBest filtering) False
spydarm addimports=T/F Whether to add identified imported modules to python module list True
trex cleandb=T/F Whether to clean up (deleted) files generated during preassembly `makedb` formatting False
trex keepblast=T/F Whether to keep the BLAST output of the repeats versus reads True
trex keeplocal=T/F Whether to keep the GABLAM local BLAST hit table of repeated versus reads True
unifake cleanup=T/F Remove TMHMM files after run True
unifake ensdat=T/F Look for acc/pep/gene in sequence name False
unifake fudgeft=T/F Fudge the real features left/right until a sequence match is found True
unifake makeindex=T/F Whether to make a uniprot index file following run False

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.