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Option Type: LIST

Argument: aamask acclist addppi alphabet altcodons altcontext altkeys altsource analyses approved archivedirs attributes backupdirs baddb baddir baddset badgenes badid badppi badtype badX baits batch blast2fas case caseft checkfields checkflanks chromcov chromspec classorder cleanfiles clustertree col combine combineppi comments complex compress conspec controls convert coreal custom datalist dbdownload dbformat dblist dbparse dbprefix dbprocess depend details detailskip direct dirlist distribute domft dropfields elements enrpairs ensdat ensgo equiv exclude experiments extlist extract fasout features fetchuid filelist flankmask fragcov ftbest ftlist ftmask ftskip genedata generics genes genotypes genspec goevidence goexcept gofilter gooddb gooddir goodmotif goodppi goodX goslim graphformats graphtypes hitdata hmm hmmoptions hmmres hublist iccut idfield idlist imask indexre indirect itunes join keepcase keywords makeclass makefreq makehmm makepages mapdb mapfields mapping mapxref maskft methodfield methodskip mismatch missing mode modlinks modules motifseq motlist musthave newheaders newscore nodefields nodelist nonaug nrchoice nrspec occfilter orftypes outlist output paramlist parentterms pathqry peptides plotft plotre plotstat posmask ppcomplex ppispec ppitype precall proteases proteome protlist ptmlist purgelist pylist query ranktypes recut reduced remslim resfile resfiles restab restrict restrictid run runid runlist runtypes samples savelocal screenelm screenmatch searchini sections seqfiles sigcut simcount simratios skipann skipgene skiplist skiploci slimcalc slimfiles slimfilter slimini slimlencut slimlist snpdrop snphead snpkeys snptabkeys snptables sourcedir specdat special speclist splitskip statfilter stylesheets subjobs taxafield taxalist taxfilter taxid taxin taxonomy taxout tdtkeys terms tofork track treeformats typefield unifake unipaths uniprotid unique unireal uparse vcodes vhost webid xnlist xref xrefdata xreflist xrefs

Modules: bob extatic humsf09 humsf10 orcfinder patis prothunter revert rje_1433 rje_aic rje_archive rje_embl rje_genomics rje_hm_html rje_hmm_V2 rje_mirna rje_pacbio rje_paml rje_price rje_slimfungo rje_taxamap slimfrap slimjim slimpid spydarm file_monster pic_html prodigis rje_dbase rje_glossary rje_itunes rje_pattern_discovery rje_pydocs rje_scansite rje_seqgen rje_seqplot slim_pickings qslimfinder_V1.9 slimbench_V1 slimfinder_V4.9 slimprob_V1.4 rje_biogrid rje_blast_V2 rje_ensembl rje_forker rje_genbank rje_genecards rje_genemap rje_go rje_hmm_V1 rje_hpc rje_hprd rje_html rje_iridis rje_mascot rje_mitab rje_motiflist rje_motif_V3 rje_ppi rje_qsub rje_samtools_V0 rje_samtools rje_seqlist rje_seq rje_slimcalc rje_slimcore rje_slimhtml rje_slimlist rje_slim rje_svg rje_taxonomy rje_tree rje_uniprot rje_xml rje_xref snp_mapper aphid budapest fiesta gablam gfessa gopher happi multihaq pagsat_V1 pagsat peptcluster pingu_V3 pingu_V4 presto_V5 qslimfinder seqmapper slimbench slimfarmer slimfinder slimmaker slimmutant slimprob slimsearch smrtscape_V1 smrtscape snapper unifake

ModuleOptionDescriptionDefault
aphid convert=LIST List of X:Y where Treatment X will be renamed Y
aphid enrpairs=LIST List of X:Y where enrichment will be restricted to X:Y ratios
aphid statfilter=LIST List of filters for data Score>-3
aphid unique=LIST Headers that, with Identifier, Treatment & Replicate, constitute unique entries Slice
bob generics=LIST List of generic motifs for Pingu analysis
bob remslim=LIST List of SLiM Types to remove (varwild/krs) varwild,krs
bob run=LIST Analyses to run (pingu/feb/mar)
bob runid=LIST List of RunIDs to include in output (all if none)
budapest clustertree=LIST List of formats for cluster tree output (3+ seqs only) text,nsf,png
budapest hitdata=LIST List of hit data to add to main budapest table prot_mass,prot_pi
budapest samples=LIST List of X:Y, where X is an iTRAQ isotag and Y is a sample
extatic altcodons=LIST List of acceptable non-AUG start codons (RNA or DNA) CTG,GTG
extatic altcontext=LIST List of contexts to be considered for altcodons XXXG
extatic orftypes=LIST List of alternative ORF types to generate (eORF/tORF/uORF/oORF/dORF) e,t,u,o
fiesta batch=LIST List of EST libraries to search (will use seqin if none given)
file_monster baddir=LIST List of "bad" directories to be automatically screened if i<1 (including subdirs)
file_monster cleanfiles=LIST List of hidden files to delete during cleanup if directory seems empty '.picasa.ini','.DS_Store'
file_monster dirlist=LIST List of directories to look in, in order of preference good -> bad for duplicates. ./
file_monster dirlist=LIST List of directories to look in, in order of preference good -> bad for duplicates. ./
file_monster extlist=LIST List of file extenstions to report individual stats for ''
file_monster filelist=X,Y,..,Z List of files of interest. Can have wildcards. *
file_monster filelist=X,Y,..,Z List of files of interest. Can have wildcards. *
file_monster gooddir=LIST List of "good" directories to be automatically kept if i<1 (including subdirs)
file_monster purgelist=LIST List of filenames (allowing wildcards) to purge (move/delete) WS_FTP.LOG
file_monster skiplist=LIST List of filenames to skip thumbs.db
file_monster skiplist=LIST List of filenames to skip thumbs.db
gablam graphtypes=LIST Formats for graph outputs (svg/xgmml/png/html) xgmml,png
gablam missing=LIST This will go through and add missing results for AccNums in FILE (or list of AccNums X,Y,..) None
gablam nrchoice=LIST Order of decisions for choosing NR sequence to keep. Otherwise keeps first sequence. (swiss/nonx/length/spec/name/acc/manual) swiss,nonx,length
gablam nrspec=LIST List of species codes in order of preference (good to bad)
gablam reduced=LIST List of terms that must be included in reduced output headers (e.g. Hit or Qry_Ordered)
gablam treeformats=LIST List of output formats for generated trees (see rje_tree.py) nwk,text,png
gfessa experiments=LIST List of (converted) experiment names to use
gopher uniprotid=LIST Extract IDs/AccNums in list from Uniprot into BASEFILE.fas and use as seqin=FILE.
happi addppi=LIST List of additional PPI pairwise files to add
happi classorder=LIST List of Class orders (otherwise alphabetical)
happi combine=LIST List of Classes to combine into Interactome for front page ('all' or '*' for all)
happi dropfields=LIST Fields to exclude from summary tables
happi genedata=LIST List of additional data tables for Gene-centric pages. Must have "Gene" or genefield field.
happi makeclass=LIST Generate classes from classorder LIST if missing from indata (go/keyword/desc/xref(+ppi)/add*) keyword
happi makepages=LIST Types of pages to make front,gene,go,mcode,class,interactome,expand
happi ppcomplex=LIST List of different evidence codes for special MCODE analyses 'Complex'
happi special=LIST Execute special analysis code for specific applications
happi stylesheets=LIST List of CSS files to use '../example.css','../redwards.css'
humsf09 direct=LIST Evidence codes for direct interactions
humsf09 generics=LIST List of pattern annotation to screen as generic motifs
humsf09 indirect=LIST Evidence codes for indirect interactions
humsf09 resfiles=LIST List of results files to read in and process
humsf09 screenelm=LIST List of ELMs to screen from CompariMotif LIG_Sin3_3,TRG_NES_1
humsf09 skipann=LIST List of auto-annotations to skip from manual annotation rand
humsf10 run=LIST List of analyses to perform (go/slim/mcl)
multihaq blast2fas=LIST List of databases to BLAST queries against prior to HAQESAC
orcfinder batch=LIST List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) *.dat,*.fas
orcfinder ftlist=LIST List of UniProt feature types to read in for analysis (default all features)
orcfinder makefreq=LIST List of types of data for which to generate frequency data (makes ftfreq file)
pagsat chromcov=LIST Report no. of chromosomes covered by a single contig at different %globID (GABLAM table) 95,98,99
pagsat fragcov=LIST List of coverage thresholds to count min. local BLAST hits (checks integrity) 50,90,95,99
pagsat treeformats=LIST Output formats for chromosome versus contig %identify UPGMA tree nwk,png
pagsat_V1 chromcov=LIST Report no. of chromosomes covered by a single contig at different %globID (GABLAM table) 95,98,99
pagsat_V1 fragcov=LIST List of coverage thresholds to count min. local BLAST hits (checks integrity) 50,90,95,99
patis nonaug=LIST Non-AUG codons to include in analysis (T or U) CTG,GTG,ACG
patis recut=LIST List of recognition sequences for restriction enzymes 'CTCGAG','GCTAGC'
peptcluster peptides=LIST These can be entered as a list or file. Lines following '#' or '>' ignored peptides.txt
peptcluster treeformats=LIST List of output formats for generated trees (nsf/nwk/text/r/png/bud/qspec/cairo/te/svg/html) nwk,text
pic_html extlist=X,Y,..,Z List of acceptable picture file extensions jpg,gif
pingu_V3 badtype=LIST List of bad interaction types, to exclude indirect_complex,neighbouring_reaction
pingu_V3 baits=LIST List of genes of interest for overlap analysis
pingu_V3 controls=LIST List of sample names that correspond to controls Control
pingu_V3 experiments=LIST List of sample names that correspond to key samples of interest
pingu_V3 goexcept=LIST List of GO ID exceptions to filtering
pingu_V3 gofilter=LIST List of GO IDs to filter out of gene lists
pingu_V3 pathqry=LIST Limit PathFinder analysis to start with given queries
pingu_V3 ppitype=LIST List of acceptable interaction types to parse out
pingu_V4 baddb=LIST PPI Types to be removed. Will only remove PPI if no support remains
pingu_V4 badppi=LIST PPI Types to be removed. Will only remove PPI if no support remains
pingu_V4 gooddb=LIST Reduce PPI to those supported by listed types
pingu_V4 goodppi=LIST Reduce PPI to those supported by listed types
pingu_V4 hublist=LIST List of hub genes to restrict pairwise PPI to
pingu_V4 mapfields=LIST List of XRef fields to use for identifier mapping (plus unifield) see docs
pingu_V4 ppispec=LIST List of PPI files/species/databases to generate PPI datasets from HUMAN
pingu_V4 taxid=LIST List of NCBI Taxa IDs to use 9606
pingu_V4 xrefdata=LIST List of files with delimited data of identifier cross-referencing (see rje_xref)
presto_V5 alphabet=X,Y,.. List of letters in alphabet of interest AAs
presto_V5 conspec=LIST List of species codes for conservation analysis. Can be name of file containing list. None
presto_V5 exclude=LIST List of files containing instances (hit,start,end) to exclude
presto_V5 goodmotif=LIST List of text to match in Motif names to keep (can have wildcards)
presto_V5 newscore=LIST Lists of X:Y, create a new statistic X, where Y is the formula of the score.
presto_V5 restrict=LIST List of files containing instances (hit,start,end) to output (only)
presto_V5 unipaths=LIST List of additional paths containing uniprot.index files from which to look for and extract features ''
prodigis proteases=LIST List of proteases to use tryp,aspn,gluc,lysc
prodigis seqfiles=LIST Sequence files for input. Wildcards permitted. RJE_SEQ filtering WILL be applied. *.fas
prothunter stylesheets=LIST List of CSS files to use 'http://www.slimsuite.unsw.edu.au/stylesheets/slimhtml.css'
qslimfinder aamask=LIST Masks list of AAs from all sequences (reduces alphabet)
qslimfinder alphabet=LIST List of characters to include in search (e.g. AAs or NTs) default AA or NT codes
qslimfinder batch=LIST List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) *.dat,*.fas
qslimfinder equiv=LIST List (or file) of TEIRESIAS-style ambiguities to use AGS,ILMVF,FYW,FYH,KRH,DE,ST
qslimfinder ftmask=LIST UniProt features to mask out (True=EM,DOMAIN,TRANSMEM)
qslimfinder imask=LIST UniProt features to inversely ("inclusively") mask. (Seqs MUST have 1+ features)
qslimfinder musthave=LIST Returned motifs must contain one or more of the AAs in LIST (reduces search space)
qslimfinder posmask=LIST Masks list of position-specific aas, where list = pos1:aas,pos2:aas 2:A
qslimfinder ptmlist=LIST List of PTM letters to add to alphabet for analysis and restrict PTM data
qslimfinder query=LIST Return only SLiMs that occur in 1+ Query sequences (Name/AccNum/Seq Number) 1
qslimfinder_V1.9 aamask=LIST Masks list of AAs from all sequences (reduces alphabet)
qslimfinder_V1.9 batch=LIST List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) *.dat,*.fas
qslimfinder_V1.9 equiv=LIST List (or file) of TEIRESIAS-style ambiguities to use AGS,ILMVF,FYW,FYH,KRH,DE,ST
qslimfinder_V1.9 ftmask=LIST UniProt features to mask out EM
qslimfinder_V1.9 imask=LIST UniProt features to inversely ("inclusively") mask. (Seqs MUST have 1+ features)
qslimfinder_V1.9 musthave=LIST Returned motifs must contain one or more of the AAs in LIST (reduces search space)
qslimfinder_V1.9 posmask=LIST Masks list of position-specific aas, where list = pos1:aas,pos2:aas 2:A
qslimfinder_V1.9 query=LIST Return only SLiMs that occur in 1+ Query sequences (Name/AccNum/Seq Number) 1
revert graphformats=LIST Formats for virus-genome graph outputs (svg/xgmml/png/html) (dev=T only) xgmml,png
revert treeformats=LIST List of output formats for generated trees (see rje_tree.py) (dev=T only) nwk,png
revert vhost=LIST List of viral hosts to output new files for. (Blank for all)
rje_1433 analyses=LIST List of analyses to perform
rje_aic coreal=LIST List of Sequence eTypes for CoreAL analysis 'AL'
rje_aic mode=LIST Run mode (refcheck/kozak/feb10/pride/jan14) pride
rje_aic nonaug=LIST List of non-AUG codons to consider in good context CTG,GTG
rje_aic output=LIST List of outputs to generate with this run all
rje_aic recut=LIST List of recognition sequences for restriction enzymes 'CTCGAG','GCTAGC'
rje_aic track=LIST List of genes or IDs to track through analysis
rje_archive archivedirs=LIST List of directories to check archive and tar/delete (should be project subdirectory full paths)
rje_archive backupdirs=LIST List of directories to backup (should be project subdirectory full paths)
rje_biogrid badtype=LIST List of bad interaction types, to exclude indirect_complex,neighbouring_reaction
rje_biogrid ppitype=LIST List of acceptable interaction types to parse out
rje_biogrid taxid=LIST List of NCBI Taxa IDs to use (for DIP and Domino) 9606
rje_biogrid vcodes=LIST List/File of viral species codes for IntAct hostvirus=T
rje_blast_V2 restab=LIST Whether to output summary results tables (Run/Search/Hit/Local/GABLAM) Search,Hit
rje_blast_V2 savelocal=LIST Whether to generate extra output for the local BLAST hits table (GFF3/SAM/TDT/TDTSEQ)
rje_dbase dbdownload=LIST List of EnsEMBL/UniProt/XML files containing details of databases to download
rje_dbase dbformat=LIST Reformats UniProt, IPI or EnsEMBL databases using RJE_SEQ
rje_dbase dbprocess=LIST List of EnsEMBL/UniProt/IPI database types to process
rje_dbase taxalist=LIST List of taxanomic groups to extract spec_codes for reduced database (else all) None
rje_embl caseft=LIST List of Features to make upper case with rest of sequence lower case
rje_embl extract=LIST Extract IDs/AccNums in list. LIST can be FILE or list of IDs/AccNums X,Y,..
rje_embl ftskip=LIST List of feature details to skip 'transl_table','translation'
rje_embl maskft=LIST List of Features to mask out
rje_embl specdat=LIST Make a DAT file of the listed species from the index (over-rules extract=LIST)
rje_ensembl chromspec=LIST List of species codes to download chromosomes for HUMAN,DROME,CAEEL,YEAST,MOUSE,DANRE,CHICK,XENTR
rje_ensembl ensdat=LIST Perform EnsDat construction of predicted UniProt data for the species listed
rje_ensembl ensgo=LIST List of species codes to make EnsGO Datasets for
rje_ensembl goevidence=LIST List of acceptable GO evidence codes. (Will use all if blank.)
rje_ensembl sections=LIST List of Ensembl sections to use for run (else All)
rje_ensembl speclist=LIST List of species to use for run (else All)
rje_forker resfile=LIST List of results files (BASEFILE.X) that will need transferring
rje_forker tofork=LIST List of system commands to fork out (standalone Forker only)
rje_genbank details=LIST List of feature details to extract into own columns
rje_genbank detailskip=LIST Subset of feature details to exclude from extraction translation
rje_genbank fasout=LIST Types of sequences to output into files (full/gene/cds/prot) as *.*.fas
rje_genbank features=LIST Subset of features to extract from Genbank file (blank for all)
rje_genbank fetchuid=LIST Genbank retrieval to of a list of nucleotide entries to generate seqin=FILE
rje_genecards altsource=LIST List of alternative sources of data (Delimited files with appropriate headers)
rje_genecards genes=LIST List of gene symbols/aliases to download
rje_genecards skiplist=LIST Skip genes matching LIST (e.g. XP_*)
rje_genemap approved=LIST Approved HGNC gene symbols to avoid over-zealous alias mapping (will add to from HGNC)
rje_genemap skiplist=LIST Skip genes matching LIST when using GeneCards website (e.g. XP_*) 'HPRD*'
rje_genemap xref=LIST Headers in Data dictionaries that are used for aliases EnsEMBL,Entrez,HGNC,HPRD,UniProt
rje_genomics tdtkeys=LIST Input fields that define unique entries Qry,Hit,AlnNum
rje_glossary terms=LIST List of terms to extract from glossary (all by default)
rje_go goslim=LIST List of GO IDs to form basis of GO Slim
rje_go parentterms=LIST Terms relating to parent relationships 'is_a','part_of'
rje_hm_html badgenes=LIST Genes to be moved to Lysate dataset
rje_hm_html dropfields=LIST Fields to exclude from summary tables
rje_hm_html makepages=LIST Types of pages to make front,gene,nested,interactome,trees,complex
rje_hm_html stylesheets=LIST List of CSS files to use '../example.css','../redwards.css'
rje_hm_html unireal=LIST Real UniProt data to add to UniFake output (Empty=None) AC,GN,RC,RX,CC,DR,PE,KW,FT
rje_hmm_V1 hmm=LIST HMM file(s). Can include wildcards. *.hmm
rje_hmm_V1 hmmoptions=LIST List or file of additional HMMer search options (joined by whitespace)
rje_hmm_V1 hmmres=LIST List of HMM search results files to convert (wildcards allowed)
rje_hmm_V1 makehmm=LIST Sequence file(s). Can include wildcards None
rje_hmm_V2 hmm=LIST HMM file(s). Can include wildcards. *.hmm
rje_hmm_V2 hmmoptions=LIST List or file of additional HMMer search options (joined by whitespace)
rje_hmm_V2 hmmres=LIST List of HMM search results files to convert (wildcards allowed)
rje_hmm_V2 makehmm=LIST Sequence file(s). Can include wildcards None
rje_hpc outlist=LIST List of extensions of outputs to add to basefile for output (basefile.*)
rje_hpc subjobs=LIST List of subjobs to farm out to HPC cluster
rje_hprd badtype=LIST List of bad interaction types, to exclude
rje_hprd ppitype=LIST List of acceptable interaction types to parse out in vitro;in vivo;yeast 2-hybrid
rje_html keywords=LIST List of keywords to put in page metadata
rje_html stylesheets=LIST List of CSS files to use 'http://www.slimsuite.unsw.edu.au/stylesheets/slimhtml.css'
rje_iridis outlist=LIST List of extensions of outputs to add to basefile for output (basefile.*)
rje_iridis subjobs=LIST List of subjobs to farm out to IRIDIS cluster
rje_itunes itunes=LIST List of itunes playlist files *.YYMMDD.tdt itunes.*.tdt
rje_mascot samples=LIST List of X:Y, where X is an iTRAQ isotag and Y is a sample
rje_mirna run=LIST List of analyses/manipulations (nrutr/enspita/cleal)
rje_mitab complex=LIST Complex identifier prefixes to expand from mapped PPI rigid
rje_mitab idfield=LIST Gene/protein identifier fields to look for
rje_mitab mapdb=LIST Restricted list of database identifier types to try mapping to xref KeyID/MapFields
rje_mitab methodfield=LIST PPI detection method fields to look for
rje_mitab taxafield=LIST Taxon identifier fields to look for
rje_mitab taxid=LIST List of NCBI Taxa IDs to use 9606
rje_mitab typefield=LIST PPI type fields to look for
rje_motif_V3 alphabet=LIST List of letters in alphabet of interest AAs
rje_motiflist conspec=LIST List of species codes for conservation analysis. Can be name of file containing list. None
rje_motiflist goodmotif=LIST List of text to match in Motif names to keep (can have wildcards)
rje_pacbio paramlist=LIST List of parameters to retain for parseparam output (file or comma separated, blank=all)
rje_pacbio xnlist=LIST Additional columns giving % sites with coverage >= Xn 1+`minanchorx`->`targetxcov`+`minanchorx`
rje_paml batch=LIST List of files to batch run on '*.fas'
rje_pattern_discovery slimfiles=LIST List of files for SLiMDisc discovery. May have wildcards. (Over-ruled by seqin=FILE.) *.fas
rje_ppi combineppi=LIST List of pairwise PPI files (using same ID set) to import. Uses Evidence field or filename
rje_ppi nodefields=LIST List of alternative A/B fields to replace Hub and Spoke fields SYMBOL_,Gene_
rje_ppi nodelist=LIST Reduce input PPI to given Node list
rje_price batch=LIST List of alignment files to use as input *.fas,*.fasta
rje_pydocs distribute=LIST Names of distributions - gets details from distributions.txt 'SLiMSuite'
rje_pydocs keywords=LIST List of keywords to add in additon to module names/descriptions
rje_pydocs methodskip=LIST List of methods to skip documentation makeInfo,cmdHelp,setupProgram,Main
rje_pydocs modlinks=LIST List of rje_ppi formats for module import links (xgmml,tdt,svg,r,png) xgmml
rje_pydocs pylist=LIST List of python modules to upload. Can have * wildcards. Will add '.py' if missing. '*'
rje_pydocs sourcedir=LIST List of subdirectories in which to look for modules tools,extras,libraries,legacy
rje_pydocs stylesheets=LIST List of style sheets to use for HTML 'rje_tabber.css','re1u06.css'
rje_qsub depend=LIST List of job ids to wait for before starting job (dependhpc=X added)
rje_qsub modules=LIST List of modules to add in job file
rje_qsub precall=LIST List of additional commands to run between module loading and program call
rje_samtools checkfields=LIST Fields in checkpos file to give Locus, Start and End for checking Locus,Start,End
rje_samtools checkflanks=LIST List of lengths flanking check regions that must also be spanned by reads 0,100,500,1000
rje_samtools skiploci=LIST List of loci to exclude from pileup parsing (e.g. mitochondria)
rje_samtools snptabkeys=LIST Fields that make unique key entries for snptable (with Locus, Pos)
rje_samtools_V0 snptables=LIST Existing SNPs of interest to be cross-referenced with the WT and Mutant SNPs
rje_scansite filelist=LIST List of files for upload. Can use wildcard. *.scansite.txt
rje_seq acclist=LIST Extract only AccNums in list. LIST can be FILE or list of AccNums X,Y,.. None
rje_seq alphabet=LIST Alphabet allowed in sequences standard 1 letter AA codes
rje_seq case=LIST List of positions to switch case, starting with first lower case (e.g case=20,-20 will have ends UC)
rje_seqgen peptides=LIST Alternative peptide sequence input for scrambling
rje_seqlist badX=LIST Exclusive filtering, removing sequences matching list
rje_seqlist goodX=LIST Inclusive filtering, only retaining sequences matching list
rje_seqplot plotft=LIST List of features to plot if input is UniProt SIGNALP,TRANSMEMBRANE,DOMAIN,PFAM
rje_seqplot plotre=LIST List of regular expressions to plot
rje_seqplot plotstat=LIST List of stats to plot (cons/rel/dis/sa/hyd) cons/rel/dis
rje_slim alphabet=LIST List of letters in alphabet of interest AAs
rje_slimcalc conspec=LIST List of species codes for conservation analysis. Can be name of file containing list. None
rje_slimcalc occfilter=LIST Same as slimfilter but for individual occurrences
rje_slimcalc slimcalc=LIST List of additional attributes to calculate for occurrences - Cons,SA,Hyd,Fold,IUP,Chg,Comp
rje_slimcalc slimfilter=LIST List of stats to filter (remove matching) SLiMs on, consisting of X*Y
rje_slimcore aamask=LIST Masks list of AAs from all sequences (reduces alphabet)
rje_slimcore alphabet=LIST List of characters to include in search (e.g. AAs or NTs) default AA or NT codes
rje_slimcore batch=LIST List of files to search, wildcards allowed. *.dat,*.fas
rje_slimcore ftmask=LIST UniProt features to mask out (True=EM,DOMAIN,TRANSMEM)
rje_slimcore imask=LIST UniProt features to inversely ("inclusively") mask. (Seqs MUST have 1+ features)
rje_slimcore motifseq=LIST Outputs fasta files for a list of X:Y, where X is the pattern and Y is the output file
rje_slimcore posmask=LIST Masks list of position-specific aas, where list = pos1:aas,pos2:aas *Also maskpos=LIST* 2:A
rje_slimcore ptmlist=LIST List of PTM letters to add to alphabet for analysis and restrict PTM data
rje_slimcore uniprotid=LIST Extract IDs/AccNums in list from Uniprot into BASEFILE.dat and use as seqin=FILE.
rje_slimfungo goslim=LIST List of GO IDs to form basis of GO Slim
rje_slimhtml baddset=LIST List of Bad Datasets to filter out of main and occ database tables
rje_slimhtml dropfields=LIST Fields to exclude from summary tables
rje_slimhtml makepages=LIST Types of pages to make front,gene,domain,rand,slim,fake,occaln,interactome,slimaln,go,nested
rje_slimhtml stylesheets=LIST List of CSS files to use '../example.css','../redwards.css'
rje_slimhtml unireal=LIST Real UniProt data to add to UniFake output (Empty=None) AC,GN,RC,RX,CC,DR,PE,KW,FT
rje_slimlist goodmotif=LIST List of text to match in Motif names to keep (can have wildcards)
rje_slimlist mismatch=LIST List of X:Y pairs for mismatch dictionary, where X mismatches allowed for Y+ defined positions
rje_slimlist slimcalc=LIST List of additional statistics to calculate for occurrences - Cons,SA,Hyd,Fold,IUP,Chg
rje_svg col=LIST Replace standard colour listing (mixed Hex and RGB)
rje_taxamap taxfilter=LIST List of taxonomic assignments to filter from rank/summary (e.g. "Uncertain")
rje_taxonomy ranktypes=LIST List of Taxon types to include if rankonly=True species,subspecies,no rank
rje_taxonomy restrictid=LIST List of Taxa IDs to restrict output to (i.e. output overlaps with taxin)
rje_taxonomy taxin=LIST List of Taxa IDs, Uniprot species codes (upper case) and/or common/scientific names
rje_taxonomy taxout=LIST List of output formats (taxid/spcode/name/common/all) taxid
rje_tree treeformats=LIST List of output formats for generated trees nwk
rje_uniprot caseft=LIST List of Features to make upper case with rest of sequence lower case
rje_uniprot dblist=LIST List of databases to extract (extract all if empty or contains 'all') see above
rje_uniprot dblist=LIST List of databases to extract (extract all if empty or contains 'all') see above
rje_uniprot dbparse=LIST List of databases to parse from DR lines in UniProtEntry object see code
rje_uniprot dbparse=LIST List of databases to parse from DR lines in UniProtEntry object see code
rje_uniprot extract=LIST Extract IDs/AccNums in list. LIST can be FILE or list of IDs/AccNums X,Y,..
rje_uniprot maskft=LIST List of Features to mask out
rje_uniprot proteome=LIST Extract complete proteomes for listed Taxa ID (e.g. 9606 for human)
rje_uniprot specdat=LIST Make a UniProt DAT file of the listed species from the index (over-rules extract=LIST)
rje_uniprot taxonomy=LIST Extract all entries for listed Taxa ID (e.g. 4751 for fungi)
rje_uniprot uparse=LIST Restricted lines to parse to accelerate parsing of large datasets for limited information
rje_xml attributes=LIST List of Attributes to exclusively extract
rje_xml elements=LIST List of Elements to exclusively extract
rje_xref altkeys=LIST Alternative fields to look for in Alias Data 'Symbol','HGNC symbol'
rje_xref badid=LIST List of XRef IDs to ignore '!FAILED!','None','N/A','-'
rje_xref comments=LIST List of comment line prefixes marking lines to ignore (throughout file) '//','%'
rje_xref compress=LIST Compress listed fields into lists (using splitchar) to allow 1:many mapping in xrefdata.
rje_xref dbprefix=LIST List of fields that should have the field added to the ID as a prefix, e.g. HGNC:0001
rje_xref idlist=LIST Subset of key IDs to map onto. (All if blank)
rje_xref join=LIST Run in join mode for list of FILE:key1|...|keyN:JoinField
rje_xref keepcase=LIST Any fields matching keepcase will retain mixed case, otherwise be converted to upper case 'Desc','Description','Name'
rje_xref mapxref=LIST List of identifiers to map to KeyIDs using mapfields
rje_xref newheaders=LIST List of new Field headers for XRefData (will replace old - must be complete)
rje_xref splitskip=LIST List of fields to bypass for field splitting 'Desc','Description','Name'
rje_xref xreflist=LIST List of XRef fields to output as sorted (unique) lists (*.*.txt) (* for all)
rje_xref xrefs=LIST List of XRef (or join) fields to keep (blank/* for all)
seqmapper mapping=LIST Possible ways of mapping sequences (in pref order) Name,AccNum,Sequence,ID,DescAcc,GABLAM,grep
seqmapper skipgene=LIST List of "genes" in protein IDs to ignore ens,nvl,ref,p,hyp,frag
slim_pickings custom=LIST Calulate Custom score as a produce of stats in LIST
slim_pickings datalist=LIST List (A,B,C) or FILE containing list of datasets for which to extract results
slim_pickings dirlist=LIST List of directories from which to extract files (wildcards OK) ./
slim_pickings indexre=LIST List of alternative regular expression patterns to try for index retrieval
slim_pickings newscore=LIST Lists of X:Y, create a new statistic X, where Y is the formula of the score.
slim_pickings protlist=LIST List (A,B,C) or FILE containing list of proteins for which to extract results
slim_pickings slimlist=LIST List (A,B,C) or FILE containing list of SLiMs (motifs) to extract
slim_pickings unipaths=LIST List of additional paths containing uniprot.index files from which to look for and extract features ''
slim_pickings webid=LIST List of SLiMDisc webserver IDs to compile. (Works only on bioware!)
slimbench flankmask=LIST List of flanking mask options (used with queries and simbench) none,win100,flank5,site
slimbench genspec=LIST Restrict ELM/OccBench datasets to listed species (restricts ELM instances)
slimbench iccut=LIST Minimum IC for (Q)SLiMFinder results for elm/sim/ppi benchmark assessment 2.0,2.1,3.0
slimbench ppispec=LIST List of PPI files/species/databases to generate PPI datasets from HUMAN,MOUSE,DROME,YEAST
slimbench resfiles=LIST List of (Q)SLiMFinder results files to use for benchmarking *.csv
slimbench runid=LIST List of factors to split RunID column into (on '.') Program,Analysis
slimbench sigcut=LIST Significance thresholds to use for assessment 0.1,0.05,0.01,0.001,0.0001
slimbench simcount=LIST Number of "TPs" to have in dataset 4,8,16
slimbench simratios=LIST List of simulated ELM:Random ratios 0,1,3,7,15,31
slimbench slimlencut=LIST List of individual SLiM lengths to return results for (0=All) 0,3,4,5
slimbench_V1 flankmask=LIST List of flanking mask options none,win300,win100,flank5,site
slimbench_V1 iccut=LIST Minimum IC for (Q)SLiMFinder results for benchmark assessment 2.0,2.1,3.0
slimbench_V1 resfiles=LIST List of (Q)SLiMFinder results files to use for benchmarking *.csv
slimbench_V1 runid=LIST List of factors to split RunID column into (on '.') 'Program','Analysis'
slimbench_V1 searchini=LIST List of INI files containing search options (should have runid setting)
slimbench_V1 sigcut=LIST Significance thresholds to use for assessment 0.05,0.01,0.001,0.0001
slimbench_V1 simcount=LIST Number of "TPs" to have in dataset 5,10
slimbench_V1 simratios=LIST List of simulated ELM:Random rations 1,4,9,19
slimbench_V1 slimlencut=LIST List of individual SLiM lengths to return results for (0=All) 0,3,4,5
slimfarmer depend=LIST List of job ids to wait for before starting job (dependhpc=X added)
slimfarmer modules=LIST List of modules to add in job file e.g. blast+/2.2.31,clustalw
slimfarmer outlist=LIST List of extensions of outputs to add to basefile for output (basefile.*)
slimfarmer precall=LIST List of additional commands to run between module loading and program call
slimfarmer subjobs=LIST List of subjobs to farm out to HPC cluster
slimfinder aamask=LIST Masks list of AAs from all sequences (reduces alphabet)
slimfinder alphabet=LIST List of characters to include in search (e.g. AAs or NTs) default AA or NT codes
slimfinder equiv=LIST List (or file) of TEIRESIAS-style ambiguities to use AGS,ILMVF,FYW,FYH,KRH,DE,ST
slimfinder ftmask=LIST UniProt features to mask out (True=EM,DOMAIN,TRANSMEM)
slimfinder imask=LIST UniProt features to inversely ("inclusively") mask. (Seqs MUST have 1+ features)
slimfinder motifseq=LIST Outputs fasta files for a list of X:Y, where X is the pattern and Y is the output file
slimfinder musthave=LIST Returned motifs must contain one or more of the AAs in LIST (reduces search space)
slimfinder posmask=LIST Masks list of position-specific aas, where list = pos1:aas,pos2:aas 2:A
slimfinder ptmlist=LIST List of PTM letters to add to alphabet for analysis and restrict PTM data
slimfinder query=LIST Return only SLiMs that occur in 1+ Query sequences (Name/AccNum)
slimfinder uniprotid=LIST Extract IDs/AccNums in list from Uniprot into BASEFILE.dat and use as seqin=FILE.
slimfinder_V4.9 aamask=LIST Masks list of AAs from all sequences (reduces alphabet)
slimfinder_V4.9 batch=LIST List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) *.dat,*.fas
slimfinder_V4.9 equiv=LIST List (or file) of TEIRESIAS-style ambiguities to use AGS,ILMVF,FYW,FYH,KRH,DE,ST
slimfinder_V4.9 ftmask=LIST UniProt features to mask out EM
slimfinder_V4.9 imask=LIST UniProt features to inversely ("inclusively") mask. (Seqs MUST have 1+ features)
slimfinder_V4.9 motifseq=LIST Outputs fasta files for a list of X:Y, where X is the pattern and Y is the output file
slimfinder_V4.9 musthave=LIST Returned motifs must contain one or more of the AAs in LIST (reduces search space)
slimfinder_V4.9 posmask=LIST Masks list of position-specific aas, where list = pos1:aas,pos2:aas 2:A
slimfinder_V4.9 query=LIST Return only SLiMs that occur in 1+ Query sequences (Name/AccNum)
slimfrap direct=LIST Evidence codes for direct interactions
slimfrap generics=LIST List of pattern annotation to screen as generic motifs
slimfrap indirect=LIST Evidence codes for indirect interactions
slimfrap resfiles=LIST List of results files to read in and process
slimfrap screenelm=LIST List of ELMs to screen from CompariMotif LIG_Sin3_3,TRG_NES_1
slimfrap skipann=LIST List of auto-annotations to skip from manual annotation rand
slimjim hublist=LIST List of hub datasets to look at (*.ppi). Can use wildcards.
slimjim runlist=LIST Optional list to limit results to certain run IDs
slimjim runtypes=LIST List of run types to generate output for (if multiple runs)
slimjim slimlist=LIST Optional list to limit results to certain SLiMs
slimjim unireal=LIST Real UniProt data to add to UniFake output (Empty=None) AC,GN,RC,RX,CC,DR,PE,KW,FT
slimmaker equiv=LIST List (or file) of TEIRESIAS-style ambiguities to use AGS,ILMVF,FYW,KRH,DE,ST
slimmutant motlist=LIST List of input SLiMs to restrict analysis to
slimmutant slimini=LIST Lists of INI file with settings for SLiMProb run. Should include runid=X and resdir=PATH.
slimpid domft=LIST List of UniProt features to treat as Domains PFAM,DOMAIN
slimprob aamask=LIST Masks list of AAs from all sequences (reduces alphabet)
slimprob alphabet=LIST List of characters to include in search (e.g. AAs or NTs) default AA or NT codes
slimprob ftmask=LIST UniProt features to mask out (True=EM,DOMAIN,TRANSMEM)
slimprob imask=LIST UniProt features to inversely ("inclusively") mask. (Seqs MUST have 1+ features)
slimprob posmask=LIST Masks list of position-specific aas, where list = pos1:aas,pos2:aas
slimprob uniprotid=LIST Extract IDs/AccNums in list from Uniprot into BASEFILE.dat and use as seqin=FILE.
slimprob_V1.4 aamask=LIST Masks list of AAs from all sequences (reduces alphabet)
slimprob_V1.4 batch=LIST List of sequence files for batch input (wildcard * permitted)
slimprob_V1.4 ftmask=LIST UniProt features to mask out EM,DOMAIN,TRANSMEM
slimprob_V1.4 imask=LIST UniProt features to inversely ("inclusively") mask. (Seqs MUST have 1+ features)
slimprob_V1.4 posmask=LIST Masks list of position-specific aas, where list = pos1:aas,pos2:aas 2:A
slimsearch aamask=LIST Masks list of AAs from all sequences (reduces alphabet)
slimsearch batch=LIST List of sequence files for batch input (wildcard * permitted)
slimsearch ftmask=LIST UniProt features to mask out EM,DOMAIN,TRANSMEM
slimsearch imask=LIST UniProt features to inversely ("inclusively") mask. (Seqs MUST have 1+ features)
slimsearch posmask=LIST Masks list of position-specific aas, where list = pos1:aas,pos2:aas 2:A
smrtscape paramlist=LIST List of parameters to retain for parseparam output (file or comma separated, blank=all)
smrtscape xnlist=LIST Additional columns giving % sites with coverage >= Xn `minanchorx`->`targetxcov`+1
smrtscape_V1 paramlist=LIST List of parameters to retain for parseparam output (file or comma separated, blank=all)
smrtscape_V1 xnlist=LIST Additional columns giving % sites with coverage >= Xn 1+`minanchorx`->`targetxcov`+`minanchorx`
snapper ftbest=LIST List of features to exclude if earlier feature in list overlaps position (see above)
snapper ftskip=LIST List of feature types to exclude from analysis source
snapper snpdrop=LIST List of SNP fields to drop
snapper snphead=LIST List of SNP file headers
snp_mapper batch=LIST List of alignment files to read X.aln - must have X_polymorphisms.txt too *.aln
snp_mapper ftbest=LIST List of features to exclude if earlier feature in list overlaps position (see above)
snp_mapper ftskip=LIST List of feature types to exclude from analysis source
snp_mapper genotypes=LIST List of snpfile headers corresponding to genotypes to map SNPs
snp_mapper screenmatch=LIST List of genotypes for which to screen out matching SNPs
snp_mapper snpdrop=LIST List of SNP fields to drop
snp_mapper snphead=LIST List of SNP file headers
snp_mapper snpkeys=LIST Additional headers to use as keys for SNP file (e.g. if mapping done by chromosome)
spydarm output=LIST List of outputs to generate release,history,updates,readme,dependencies
spydarm pylist=LIST List of python modules to upload. Can have * wildcards. Will add '.py' if missing. '*'
spydarm sourcedir=LIST List of subdirectories in which to look for modules tools,extras,libraries,legacy
unifake features=LIST List of files of addtional features in delimited form
unifake unifake=LIST List of predictions to add to entries tmhmm,signalp,disorder,pfam,uniprot
unifake unireal=LIST Real UniProt data to add to UniFake output 'AC','GN','RC','RX','CC','DR','PE','KW'

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