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Option Type: FILE

Argument: aadimerfreq aadis aafreq aaprop acctable addalias addppi addquery aliases aliasfile altcontrol altdis altpam alttreatment archived arraydata assembly background backupdb basefile batchout biogrid biomart blastd blasti blasto blastopt blastres buildfile cardout compdb control ctlfile cwtree data datout datpickup dbindex ddi dip disin dmidata dmifile domfilter domino domtable dormant elm elmclass elmdat elmdomains elminstance elminteractors elmpfam embldat ensloci equivout errorlog evidence expconvert fam fasdb fastq filexref filterout focus ftfile ftfreq ftgablam ftout gablam gablamdis genbase genecards genemap genepickle genome godata goids gomap haqbat haqdb haqmatrix hgncdata hgncmap hhpid hivseq hmmout hmmtab homeback iini indata infile info intact ipilinks jobini larrow linkout litfile loadmatrix log makedb mapdb mapdna mapseq mascot megaslim mgcfile mgidata mint miranda mitab motifout motifs motinfo msfile mutfile mutpileup namemap nandr negatives netphos newres nsfin obofile occbenchpos occdata occfile occres omim orthdb outfile pairwise pamfile pamout parse pdbdata pelm pelmfas peptides pfam pfamdata phosblast phosres phyoptions picback picdesc pichome pickledata pileup pillars pingupickle positives posmatrix ppi ppifile ppiout preassembly pridefile projects protdesc protdist qblast qryspec qseqfile qslimfinder querydb queryppi queryseq randres randsource rarrow reactome readcheck reference refgenome refseq relcons resfile restin savedis savetree scansite scapback screenddi screenfile searchdb searchini seqdb seqin seqout signalp singlesf slimcheck slimdesc slimres snpfile snpmap snptable source sourcedata specfile spectdt sqldump tabber tabout tagfile tagindex tagmap taxadb taxmap tdtfile titletext tmhmm treatment uniprot unispec validated vnematrix wtpileup xmerback xmerfile xmerseq xref xrefdata

Modules: bob diploidocus humsf09 jrj_fastq orcfinder patis revert rje_1433 rje_aic rje_archive rje_embl rje_genomics rje_hivqsf rje_hm_html rje_hmm_V2 rje_mirna rje_misc rje_omim rje_pacbio rje_paml rje_price rje_slimfungo rje_spf rje_taxamap samphaser scap slimdip slimfrap slimgoer slimjim slimpid trex compass peptide_dismatrix peptide_stats pic_html prodigis rje_dbase rje_glossary rje_mysql rje_pattern_discovery rje_phos rje_scansite rje_seqgen rje_seqplot rje_yeast seqforker sfmap2png slim_pickings wormpump gopher_V2 qslimfinder_V1.9 slimbench_V1 slimfinder_V4.9 slimprob_V1.4 rje_aaprop rje_biogrid rje_blast_V1 rje_blast_V2 rje_blast rje_dismatrix_V2 rje_dismatrix_V3 rje_ensembl rje_genbank rje_genecards rje_genemap rje_go rje_hmm_V1 rje_hpc rje_html rje_iridis rje_markov rje_mascot rje_mitab rje_motiflist rje_obj rje_pam rje_ppi rje_samtools_V0 rje_samtools rje_seqlist rje_seq rje_slimcalc rje_slimcore rje_slimhtml rje_slimlist rje_synteny rje_taxonomy rje_tm rje_tree rje_uniprot rje_xml rje rje_xref snp_mapper aphid badasp budapest comparimotif_V3 fiesta gablam gasp gfessa gopher happi haqesac multihaq pagsat_V1 pagsat peptcluster picsi pingu_V3 pingu_V4 presto_V5 qslimfinder seqmapper slimbench slimfarmer slimfinder slimmutant slimparser slimprob slimsearch smrtscape_V1 smrtscape snapper unifake

ModuleOptionDescriptionDefault
aphid data=FILE Delimited file containing input data None
aphid seqin=FILE Sequence file containing hits (if pepnorm != count) None
badasp log=FILE Redirect log to FILE Default = calling_program.log or basefile.log
badasp pamfile=FILE Sets PAM1 input file jones.pam
bob motifs=FILE File of motifs for selected analysis
bob newres=FILE Name for new results file *.bob.csv
bob randres=FILE File with results of random SLiMFinder runs. Will use for DS significance assessment. None
bob slimres=FILE Name of SLiMFinder results file
budapest haqdb=FILE Optional additional search database for MultiHAQ analysis None
budapest mascot=FILE Name of MASCOT csv file None
budapest searchdb=FILE Fasta file for GABLAM search of EST translations None
budapest seqin=FILE Name of EST fasta file used for search None
comparimotif_V3 aafreq=FILE Use FILE to replace uniform AAFreqs (FILE can be sequences or aafreq) None
comparimotif_V3 motifs=FILE File of input motifs/peptides None
comparimotif_V3 motinfo=FILE Filename for output of motif summary table (if desired) None
comparimotif_V3 resfile=FILE Name of results file, FILE.compare.tdt. motifsFILE-searchdbFILE.compare.tdt
comparimotif_V3 searchdb=FILE (Optional) second motif file to compare. Will compare to self if none given. None
compass netphos=FILE Motif prediction files for sequences in netphos format *.netphos
compass scansite=FILE Motif prediction files for sequences in scansite format *.scansite, *.automotif & *.elm
compass signalp=FILE SignalP results in single-line format *.signalp
compass tmhmm=FILE Transmembrane topology data in TMHMM single-line format *.tmhmm
compass uniprot=FILE Sequence features/details in UniProt download format *.uniprot
diploidocus basefile=FILE Root of output file names diploidocus
fiesta blastopt=FILE File containing additional BLAST options for run, e.g. -B F None
fiesta querydb=FILE File of query sequences to search for in EST library None
fiesta searchdb=FILE Fasta file for GABLAM search of EST translations None
fiesta seqin=FILE EST file to be processed None
gablam blastres=FILE BLAST results file for input (over-rides seqin and searchdb) None
gablam searchdb=FILE Database to search. By default, same as seqin
gablam seqin=FILE Query dataset file infile.fas
gasp nsfin=FILE Newick Standard Format treefile infile.nsf
gasp seqin=FILE Fasta/ClustalW/Phylip Format sequence file infile.fas
gfessa expconvert=FILE File containing 'Header', 'Experiment' conversion data None
gfessa seqin=FILE File containing EST/cDNA data to search for tags within None
gfessa tagfile=FILE File containing SuperSAGE tags and counts None
gfessa tagindex=FILE File containing possible tags and sequence names from seqin file *.tag.index
gfessa tagmap=FILE Tag to sequence mapping file to over-ride auto-generated file based on Seqin and Mismatch None
gopher orthdb=FILE Fasta file with pool of sequences for orthology discovery
gopher orthdb=FILE Fasta file with pool of sequences for orthology discovery
gopher seqin=FILE Fasta file of 'query' sequences for orthology discovery (over-rides uniprotid=LIST)
gopher unispec=FILE UniProt species file for TaxaID conversion. Will use TaxaID instead of Species Code if given None
gopher_V2 orthdb=FILE Fasta file with pool of sequences for orthology discovery
gopher_V2 orthdb=FILE Fasta file with pool of sequences for orthology discovery
gopher_V2 seqin=FILE Fasta file of 'query' sequences for orthology discovery
happi gablam=FILE Delimited GABLAM results file for homology data basefile.gablam.tdt
happi godata=FILE Delimited file of GO Data (Gene,GO_ID,GO_Type,GO_Desc) basefile.go.tdt
happi indata=FILE Input data for front pages
happi pairwise=FILE Pairwise protein-protein interation (PPI) file
happi titletext=FILE File containing (Page,ID,Title) for mouseover text titletext.tdt
happi xrefdata=FILE File of Database cross-references. Must have "Gene" field.
haqesac fasdb=FILE Fasta format database to extract sequences from None
haqesac haqmatrix=FILE File of AA vs AA scores used in SAQ and PAQ. None
haqesac log=FILE Redirect log to FILE Default = calling_program.log or basefile.log
haqesac pamfile=FILE Sets PAM1 input file jones.pam
haqesac phyoptions=FILE File containing extra Phylip tree-making options ('batch running') to use None
haqesac protdist=FILE File containing extra Phylip PROTDIST ('batch running') to use None
haqesac qblast=FILE BLAST database against which to BLAST query (see rje_blast.py options) [None] 'blaste=1e-7','blastv=1000,blastb=0'
haqesac qseqfile=FILE Sequence file from which to extract query (query=X) and peform BLAST None
humsf09 domtable=FILE Table of domain predictions None
humsf09 elm=FILE File of ELM Motifs None
humsf09 nandr=FILE File of Neduva & Russell motifs None
humsf09 pairwise=FILE Pingu Pairwise PPI file None
humsf09 pickledata=FILE Genemap pickle to import and use. (See other rje_genemap options) None
jrj_fastq basefile=FILE Base name for output (input by default) None
jrj_fastq fastq=FILE Input FASTQ file for analysis None
multihaq seqin=FILE Input query sequences None
orcfinder altdis=FILE Alternative all by all distance matrix for relationships None
orcfinder ftfreq=FILE File containing UPC frequencies of relevant feature subcategories None
orcfinder gablamdis=FILE Alternative GABLAM results file None
orcfinder resfile=FILE Main SLiMFinder results table slimfinder.csv
orcfinder seqin=FILE Sequence file to search None
pagsat assembly=FILE Fasta file of assembled contigs to assess None
pagsat refgenome=FILE Fasta file of reference genome for assessment (also *.gb for full functionality) None
pagsat_V1 assembly=FILE Fasta file of assembled contigs to assess None
pagsat_V1 refgenome=FILE Fasta file of reference genome for assessment (also *.gb for full functionality) None
patis mgcfile=FILE Name of the MGC clone sequence file mgc_clones.human.fasta
peptcluster aadis=FILE Alternative amino acid distance matrix None
peptcluster aaprop=FILE File of amino acid properties aaprop.txt
peptcluster savedis=FILE Output distance matrix to file peptides.*
peptcluster savetree=FILE Save generated tree as FILE peptides.peptdis.peptcluster.*
peptide_dismatrix aaprop=FILE Amino Acid property matrix file. aaprop.txt
peptide_stats aaprop=FILE Amino Acid property matrix file. aaprop.txt
pic_html homeback=FILE File to use for picture home background None
pic_html larrow=FILE Image file for Left Arrow (pref GIF) larrow.gif
pic_html picback=FILE File to use for other page backgrounds None
pic_html picdesc=FILE File with picture descriptions Type:Group:Element Description pic_descriptions.txt
pic_html pichome=FILE File name for pictures home page pictures.htm
pic_html rarrow=FILE Image file for Right Arrow (pref GIF) rarrow.gif
picsi basefile=FILE Base for output files picsi
picsi qryspec=FILE Species code for Query species EMIHU
picsi seqin=FILE File containing sequences hit during searches None
picsi spectdt=FILE File of UniProt species translations '/scratch/RJE_Filestore/SBSBINF/Databases/DBase_090505/UniProt/uniprot.spec.tdt'
pingu_V3 addalias=FILE Extra (manual?) aliases to add to GeneMap object following loading of pickles etc. None
pingu_V3 addppi=FILE Add additional PPI from a simple delimited file IDA,IDB,Evidence None
pingu_V3 biogrid=FILE BioGRID flat file None
pingu_V3 dip=FILE DIP interactions flat file None
pingu_V3 domino=FILE Domino interactions flat file None
pingu_V3 ensloci=FILE File of EnsEMBL genome EnsLoci treatment
pingu_V3 evidence=FILE Mapping file for evidence terms None
pingu_V3 genepickle=FILE Pickled GeneMap object. Alternatively, use below commands to make GeneMap object None
pingu_V3 intact=FILE IntAct flat file None
pingu_V3 ipilinks=FILE IPI Links file with 'IPI', 'Symbol' and 'EnsG' fields
pingu_V3 mint=FILE MINT flat file None
pingu_V3 pairwise=FILE Load interaction data from existing Pingu Pairwise file None
pingu_V3 pfamdata=FILE Delimited files containing domain organisation of sequences None
pingu_V3 pingupickle=FILE Full path to Pingu pickle file to look for/use/save pingu.pickle
pingu_V3 qslimfinder=FILE File containing sequences matching Sample names for Query SLiMFinder runs None
pingu_V3 reactome=FILE Reactome interactions flat file None
pingu_V3 screenddi=FILE Whether to screen out probably domain-domain interactions from file None
pingu_V4 biogrid=FILE BioGRID flat file None
pingu_V4 dip=FILE DIP interactions flat file None
pingu_V4 domino=FILE Domino interactions flat file None
pingu_V4 evidence=FILE Mapping file for evidence terms None
pingu_V4 intact=FILE IntAct flat file None
pingu_V4 mint=FILE MINT flat file None
pingu_V4 ppiout=FILE Save pairwise PPI file following processing (if rest=None) None
pingu_V4 queryppi=FILE Load a file of 'Query','Hub' PPI and generate expanded PPI Datasets in PPI.*/ None
pingu_V4 queryseq=FILE Fasta file containing the Query protein sequences corresponding to QuerySeq *.fas
pingu_V4 reactome=FILE Reactome interactions flat file None
presto_V5 aaprop=FILE Amino Acid property matrix file. aaprop.txt
presto_V5 domfilter=FILE Use the DomFilter options, reading domains from FILE None
presto_V5 motifout=FILE Filename for output of reformatted (and filtered?) motifs in PRESTO format None
presto_V5 motifs=FILE File of input motifs/peptides None
presto_V5 posmatrix=FILE Score matrix for amino acid combinations used in pos weighting. (conscore=pos builds from propmatrix) None
presto_V5 searchdb=FILE Protein Fasta file to search (or second motif file to compare) None
prodigis peptides=FILE File containing list of identified peptides None
prodigis positives=FILE File of positively identified proteins matching peptide lists None
prodigis source=FILE File containing source protein data (including UniProt AccNum column) None
qslimfinder aadimerfreq=FILE Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) (!!!Experimental!!!) None
qslimfinder aafreq=FILE Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) None
qslimfinder addquery=FILE Adds query sequence(s) to batch jobs from FILE None
qslimfinder altdis=FILE Alternative all by all distance matrix for relationships None
qslimfinder focus=FILE FILE containing focal groups for SLiM return (see Manual for details) None
qslimfinder gablamdis=FILE Alternative GABLAM results file None
qslimfinder megaslim=FILE Make/use precomputed results for a proteome (FILE) in fasta format None
qslimfinder negatives=FILE Multiply raw probabilities by under-representation in FILE (!!!Experimental!!!) None
qslimfinder resfile=FILE Main QSLiMFinder results table qslimfinder.csv
qslimfinder seqin=FILE Sequence file to search None
qslimfinder slimcheck=FILE Motif file/list to add to resfile output
qslimfinder_V1.9 aadimerfreq=FILE Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) (!!!Experimental!!!) None
qslimfinder_V1.9 aafreq=FILE Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) None
qslimfinder_V1.9 addquery=FILE Adds query sequence(s) to batch jobs from FILE None
qslimfinder_V1.9 altdis=FILE Alternative all by all distance matrix for relationships None
qslimfinder_V1.9 focus=FILE FILE containing focal groups for SLiM return (see Manual for details) None
qslimfinder_V1.9 gablamdis=FILE Alternative GABLAM results file None
qslimfinder_V1.9 negatives=FILE Multiply raw probabilities by under-representation in FILE (!!!Experimental!!!) None
qslimfinder_V1.9 resfile=FILE Main QSLiMFinder results table qslimfinder.csv
qslimfinder_V1.9 seqin=FILE Sequence file to search None
qslimfinder_V1.9 slimcheck=FILE Motif file/list to add to resfile output
revert aliasfile=FILE Delimited file of 'Name','Alias' to use in place of batch summary files *.alias.tdt
revert basefile=FILE Root of output files. Defaults to `virusgb.genome` if blank/None None
revert genome=FILE Fasta file containing contigs or chromosomes of host genome genome.fas
revert searchdb=FILE Fasta file of viral (& host?) proteins for assembly annotation. Use viral proteins if None.
rje errorlog=FILE If given, will write errors to an additional error file. None
rje log=FILE Redirect log to FILE Default = calling_program.log
rje_1433 litfile=FILE File of literature interactions 1433_Lit.tdt
rje_1433 msfile=FILE File containing MS Data 1433_msdata_full.txt
rje_aaprop aaprop=FILE Amino Acid property matrix file. aaprop.txt
rje_aic biomart=FILE File containing BioMart download
rje_aic pridefile=FILE Delimited file containing PRIDE IDs and Protein IDs
rje_aic refseq=FILE File containing RefSeq download in GenBank format
rje_archive archived=FILE File to output archive summaries into 'BASEFILE.archived.tdt'
rje_archive backupdb=FILE File to output backup summaries into 'BASEFILE.backups.tdt'
rje_archive basefile=FILE This will set the 'root' filename for output files (FILE.*), including the log 'rds'
rje_archive dormant=FILE File to output dormant directories into 'BASEFILE.dormant.tdt'
rje_archive projects=FILE Delimited file of `Project` and `RDS` code. If provided, will not use rds=X 'projects.tdt'
rje_biogrid genecards=FILE File of links between IDs. For human, should have HGNC and EnsLoci columns. None
rje_biogrid ppifile=FILE PPI database flat file None
rje_biogrid seqin=FILE Sequence file containing protein sequences with appropriate Accession Numbers/IDs None
rje_blast blastd=FILE BLAST database (BLAST -d FILE) None
rje_blast blasti=FILE Input file (BLAST -i FILE) None
rje_blast blasto=FILE Output file (BLAST -o FILE) *.blast
rje_blast blastopt=FILE File containing raw BLAST options (applied after all others)
rje_blast_V1 blastd=FILE BLAST database (BLAST -d FILE) None
rje_blast_V1 blasti=FILE Input file (BLAST -i FILE) None
rje_blast_V1 blasto=FILE Output file (BLAST -o FILE) *.blast
rje_blast_V1 blastopt=FILE File containing raw BLAST options (applied after all others)
rje_blast_V2 blastd=FILE BLAST database (BLAST -d FILE) None
rje_blast_V2 blasti=FILE Input file (BLAST -i FILE) None
rje_blast_V2 blasto=FILE Output file (BLAST -o FILE) *.blast
rje_blast_V2 blastopt=FILE File containing raw BLAST options (applied after all others)
rje_dbase makedb=FILE Makes a database from combined databases None
rje_dbase taxadb=FILE File containing details of taxanomic sub-databases to make None
rje_dismatrix_V2 loadmatrix=FILE Loads a matrix from FILE None
rje_dismatrix_V3 loadmatrix=FILE Loads a matrix from FILE None
rje_embl datout=FILE Name of new (reduced) DAT file of extracted sequences None
rje_embl dbindex=FILE Database index file uniprot.index
rje_embl embldat=FILE Name of EMBL file None
rje_embl ftout=FILE Outputs table of features into FILE None
rje_embl linkout=FILE Table of extracted Database links None
rje_embl tabout=FILE Table of extracted details None
rje_ensembl datpickup=FILE Text file containing names of proteins already processed (skip and append) ensdat.txt
rje_ensembl goids=FILE File containing GO IDs GO.terms_ids_obs
rje_ensembl hgncmap=FILE File to be used for HGNC ID mapping
rje_ensembl pfam=FILE Path to PFam LS file /home/richard/Databases/PFam/Pfam_ls
rje_ensembl signalp=FILE Path to SIGNALP program /home/richard/Bioware/signalp-3.0/signalp
rje_ensembl tmhmm=FILE Path to TMHMM program /home/richard/Bioware/TMHMM2.0c/bin/tmhmm
rje_ensembl unispec=FILE Alternative UniProt species file None
rje_genbank basefile=FILE Root of output file names (same as input file by default)
rje_genbank seqin=FILE Input Genbank file
rje_genecards cardout=FILE File for output of genecard data genecards.tdt
rje_genecards ensloci=FILE File of EnsLoci genome to incorporate /home/richard/Databases/EnsEMBL/ens_HUMAN.loci.fas
rje_genecards hgncdata=FILE HGNC download file containing data
rje_genemap aliases=FILE Files containing aliases only.
rje_genemap ensloci=FILE File of EnsLoci genome to incorporate None
rje_genemap genepickle=FILE Use pickle of GeneMap data without additional loading/processing etc. None
rje_genemap hgncdata=FILE Download file containing HGNC data.
rje_genemap mgidata=FILE Download file containing MGI data (ftp://ftp.informatics.jax.org/pub/reports/MGI_MouseHumanSequence.rpt)
rje_genemap pfamdata=FILE Delimited files containing domain organisation of sequences None
rje_genemap pickledata=FILE Genemap pickle to import and use.
rje_genemap sourcedata=FILE File containing data in order of preference regarding conflicting data.
rje_genomics tdtfile=FILE Input delimited text file with data to convert None
rje_glossary infile=FILE Input file of Term:Definition glossary.tdt
rje_glossary outfile=FILE Output file name (input.html by default)
rje_go obofile=FILE Input GO OBO V1.2 download None
rje_hivqsf genemap=FILE Delimited human gene mapping data
rje_hivqsf hhpid=FILE Delimited text file containing HHPID interactions
rje_hivqsf hivseq=FILE File containing HIV sequences
rje_hm_html titletext=FILE File containing (Page,ID,Title) titletext.tdt
rje_hmm_V1 hmmout=FILE Pipe results of HMM searches into FILE None
rje_hmm_V1 hmmtab=FILE Delimited table of results ('None' to skip) searchdb.tdt
rje_hmm_V1 searchdb=FILE Fasta file to search with HMMs None
rje_hmm_V2 hmmout=FILE Pipe results of HMM searches into FILE None
rje_hmm_V2 hmmtab=FILE Delimited table of results ('None' to skip) searchdb.tdt
rje_hmm_V2 searchdb=FILE Fasta file to search with HMMs None
rje_hpc jobini=FILE Ini file to pass to the called program None
rje_hpc seqin=FILE Input sequence file to farm out None
rje_html tabber=FILE Tabber javascript file location 'tabber.js'
rje_iridis iini=FILE Ini file to pass to the called program None
rje_iridis resfile=FILE Main output file for iX run islimfinder.csv
rje_iridis resfile=FILE Main output file for iX run islimfinder.csv
rje_iridis resfile=FILE Main output file for iX run islimfinder.csv
rje_iridis seqin=FILE Input sequence file to farm out None
rje_markov aafreq=FILE Generate expected 1mer frequencies from FILE of aafreq None
rje_markov seqin=FILE File with input sequences None
rje_markov xmerfile=FILE File from which to load Xmer counts and build suffix tree None
rje_mascot mascot=FILE Name of MASCOT csv file None
rje_mirna arraydata=FILE File of array data for Cleal analysis
rje_mirna miranda=FILE Miranda prediction file
rje_mirna seqin=FILE Main file for analysis, containing UTRs
rje_mirna validated=FILE Validate mRNA target file
rje_misc infile=FILE Name of input file for relevant task None
rje_mitab mitab=FILE MITAB interaction file
rje_motiflist aaprop=FILE Amino Acid property matrix file. aaprop.txt
rje_motiflist domfilter=FILE Use the DomFilter options, reading domains from FILE None
rje_motiflist motifs=FILE File of input motifs/peptides None
rje_motiflist posmatrix=FILE Score matrix for amino acid combinations used in pos weighting. (conscore=pos builds from propmatrix) None
rje_mysql buildfile=FILE Output file for MySQL Build statements mysql_build.txt
rje_mysql sqldump=FILE Read in an SQL dump file and convert into CSV None
rje_obj errorlog=FILE If given, will write errors to an additional error file. None
rje_obj log=FILE Redirect log to FILE Default = calling_program.log
rje_omim omim=FILE Input file (OMIM text download) 'omim.txt'
rje_pacbio seqin=FILE Subread sequence file for analysis None
rje_pam altpam=FILE Alternative to PAM file input = matrix needing scaling by aafreq None
rje_pam pamout=FILE Name for rescaled PAM matrix output *.pam named after altpam=FILE
rje_pam seqin=FILE Sequence file from which to calculate AA freq for scaling None
rje_paml ctlfile=FILE PAML control file to use 'codeml.ctl'
rje_paml infile=FILE Name for PAML sequence input file 'infile'
rje_paml outfile=FILE Name of PAML output file 'mlc'
rje_pattern_discovery batchout=FILE Create a batch file containing individual seqin=FILE calls. None
rje_pattern_discovery info=FILE Calculate information content of motifs in FILE (based on AA Freq from seqin, if given) None
rje_pattern_discovery outfile=FILE Output file name seqin.teiresias.*
rje_pattern_discovery seqin=FILE Sequence File to search None
rje_phos pelm=FILE Filename for phosphoELM download None
rje_phos pelmfas=FILE Filename for fasta file output of pELM sequences pelm.fas
rje_phos phosblast=FILE Fasta file of sequences to perform phosBLAST method against pELM None
rje_phos phosres=FILE Delimited text file containing input sequence, position and evidence *.phosres.tdt
rje_ppi pairwise=FILE Input PPI pairwise file, containing Hub, Spoke and optional Evidence columns
rje_price resfile=FILE Results file price.tdt
rje_price seqin=FILE Input sequence alignment in fasta format (over-rides batch=LIST) None
rje_samtools altcontrol=FILE MPileup or processed TDT file to be used for control SNP frequencies in Alt genome
rje_samtools alttreatment=FILE MPileup or processed TDT file to be used for treatment SNP frequencies in Alt genome
rje_samtools control=FILE MPileup or processed TDT file to be used for control SNP frequencies
rje_samtools readcheck=FILE SAM/Pileup/RID file with read mappings None
rje_samtools snptable=FILE Table of SNPs of cross-reference with FDR SNP output
rje_samtools treatment=FILE MPileup or processed TDT file to be used for treatment SNP frequencies
rje_samtools_V0 mutpileup=FILE MPileup results for mutant genome resequencing None
rje_samtools_V0 wtpileup=FILE MPileup results for wildtype genome resequencing None
rje_scansite outfile=FILE Output file name scansite.tdt
rje_seq fasdb=FILE Fasta format database to extract sequences from None
rje_seq filterout=FILE Saves filtered sequences (as fasta) into FILE. *NOTE: File is appended if append=T* None
rje_seq haqbat=FILE Generate a batch file (FILE) to run HAQESAC on generated BLAST files, with seqin as queries None
rje_seq mapdna=FILE Map DNA sequences from FILE onto sequences of same name in protein alignment None
rje_seq mapseq=FILE Maps sequences from FILE to sequences of same name None
rje_seq relcons=FILE Returns a file containing Pos AbsCons RelCons None
rje_seq seqin=FILE Loads sequences from FILE (fasta,phylip,aln,uniprot or fastacmd names from fasdb) None
rje_seq seqout=FILE Saves 'tidied' sequences to FILE after loading and manipulations None
rje_seqgen aafreq=FILE File from which to read AA Freqs None
rje_seqgen outfile=FILE Output delimited file of scrambled peptides or peptide and scrambled sequence. scramble.tdt
rje_seqgen screenfile=FILE File of Xmers to screen in generated sequences None
rje_seqgen seqin=FILE Input sequence file to randomise None
rje_seqgen xmerfile=FILE File from which to read Xmer frequencies for sequence generation None
rje_seqgen xmerseq=FILE Sequence file from which to calculate Xmer frequencies None
rje_seqlist seqdb=FILE Sequence file from which to extract sequences (fastacmd/index formats) None
rje_seqlist seqin=FILE Sequence input file name. None
rje_seqlist seqout=FILE Whether to output sequences to new file after loading and filtering None
rje_seqplot occfile=FILE File containing motif occurrences to plot None
rje_seqplot seqin=FILE File containing input sequences None
rje_slimcalc aaprop=FILE Amino Acid property matrix file. aaprop.txt
rje_slimcalc orthdb=FILE File to use as source of orthologues for GOPHER
rje_slimcalc posmatrix=FILE Score matrix for amino acid combinations used in pos weighting. (conscore=pos builds from propmatrix) None
rje_slimcalc vnematrix=FILE BLOSUM matrix file to use for VNE relative conservation
rje_slimcore aafreq=FILE Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) None
rje_slimcore altdis=FILE Alternative all by all distance matrix for relationships None
rje_slimcore domtable=FILE Domain table containing domain ("Type") and sequence ("Name") pairings for additional UPC None
rje_slimcore equivout=FILE File for equivalence list output equiv.txt
rje_slimcore gablamdis=FILE Alternative GABLAM results file None
rje_slimcore megaslim=FILE Make/use precomputed results for a proteome (FILE) in fasta format None
rje_slimcore randsource=FILE Source for new sequences for random datasets (replaces UPCs) None
rje_slimcore seqin=FILE Sequence file to search. Over-rules batch mode (and uniprotid=LIST). None
rje_slimfungo gomap=FILE Mapping of sequences to GO categories None
rje_slimfungo obofile=FILE Input GO OBO V1.2 download None
rje_slimfungo occdata=FILE File of motif occurrences. Must have None
rje_slimfungo seqin=FILE File of input sequences None
rje_slimhtml slimdesc=FILE File containing descriptions for SLiMs slimdesc.txt
rje_slimhtml titletext=FILE File containing (Page,ID,Title) titletext.tdt
rje_slimlist motifout=FILE Name of output file for reformatted/filtered SLiMs (PRESTO format) None
rje_slimlist motifs=FILE File of input motifs/peptides None
rje_slimlist motinfo=FILE Filename for output of motif summary table (if desired) None
rje_spf infile=FILE The input SPF file input.spf
rje_spf log=FILE The name of the output log (*.log) rje_spf.log
rje_synteny basefile=FILE Basename for output files ftgablam basefile
rje_synteny ftfile=FILE File of reference genome features *.Feature.tdt
rje_synteny ftgablam=FILE GABLAM search results (e.g. from PAGSAT) of Genes/Proteins against assembly regions None
rje_synteny refgenome=FILE Fasta/Genbank file of reference genome for assessment (also *.gb for full functionality) None
rje_taxamap protdesc=FILE Delimited file of protein, description None
rje_taxonomy namemap=FILE NCBI Name mapping file names.dmp
rje_taxonomy specfile=FILE Uniprot species code download. speclist.txt
rje_taxonomy taxmap=FILE NCBI Node Dump File nodes.dmp
rje_tm seqin=FILE Sequence file for which predictions have been made None
rje_tm signalp=FILE SignalP output file None
rje_tm tmhmm=FILE TMHMM output file None
rje_tree cwtree=FILE Make a ClustalW NJ Tree from FILE (will save *.ph or *.phb) None
rje_tree disin=FILE load distance matrix from FILE (Phylip format for use with distance matrix methods) None
rje_tree phyoptions=FILE File containing extra Phylip tree-making options ('batch running') to use None
rje_tree protdist=FILE File containing extra Phylip PROTDIST options ('batch running') to use None
rje_tree savetree=FILE Save a generated tree as FILE seqin.maketree.nsf
rje_uniprot acctable=FILE Delimited text file from which to retrieve a list of accession numbers None
rje_uniprot dbindex=FILE Database index file uniprot.index
rje_uniprot uniprot=FILE Name of UniProt file None
rje_xml parse=FILE Source file for reading XML file None
rje_xref filexref=FILE File to XRef and expand with xrefs before re-saving
rje_yeast pillars=FILE YGOB pillars file Pillars.tab
rje_yeast ppifile=FILE Input PPI data (two columns of binary interactors) Y2H_union.txt
rje_yeast seqin=FILE Input sequence file containing yeast sequences Proteins.fas
rje_yeast xref=FILE Yeast identifier XRef file (e.g. BioMart download) yeast_xref.20101222.tdt
samphaser basefile=FILE Root of output file names (same as Pileup input file by default)
samphaser pileup=FILE Pileup file of reads against input genome.
scap scapback=FILE File with sequences for background SCAP calculations None
scap seqin=FILE File with input sequences for testing None
scap xmerback=FILE File with sequences for background Markov Chain calculations (can be pickle) seqin
seqforker log=FILE Redirect log to FILE Default = calling_program.log
seqforker seqin=FILE Input sequence file None
seqmapper basefile=FILE Set resfile=FILE and log=FILE at the same time
seqmapper mapdb=FILE File of sequences to map sequences onto None
seqmapper resfile=FILE Base of output filenames (*.mapped.fas, *.missing.fas & *.mapping.tdt) seqin.mapdb
seqmapper seqin=FILE File of sequences to be mapped None
sfmap2png seqin=FILE *.mapping.fas file to use as input data
slim_pickings datout=FILE Extract UniProt entries from parent proteins where possible into FILE uniprot_extract.dat
slim_pickings ftout=FILE Make a file of UniProt features for extracted parent proteins, where possible, incoroprating SLIMs None
slim_pickings occres=FILE Output individual occurrence data in FILE None
slim_pickings outfile=FILE Name of output file. slimdisc_results.csv
slimbench compdb=FILE Motif file to be used for benchmarking elmclass file
slimbench elmclass=FILE Download from ELM website of ELM classes elm_classes.tsv
slimbench elmdat=FILE File of downloaded UniProt entries (See rje_uniprot for more details) 'ELM.dat'
slimbench elmdomains=FILE Download from ELM website of ELM Pfam domain interactors elm_interaction_domains.tsv
slimbench elminstance=FILE Download from ELM website of ELM instances elm_instances.tsv
slimbench elminteractors=FILE Download from ELM website of ELM interactors elm_interactions.tsv
slimbench occbenchpos=FILE File of all positive occurrences for OccBench genpath/ELM_OccBench/ELM.full.ratings.csv
slimbench randsource=FILE Source for random/simulated dataset sequences. If species, will extract from UniProt HUMAN
slimbench searchini=FILE INI file containing SLiMProb search options that restrict returned positives
slimbench_V1 compdb=FILE Motif file to be used for benchmarking (default = reduced elmclass file)
slimbench_V1 dmidata=FILE File of 3DID DMI data '3did.DMI.csv'
slimbench_V1 elmclass=FILE Download from ELM website of ELM classes 'elm_classes.tsv'
slimbench_V1 elminstance=FILE Download from ELM website of ELM instances 'elm_instances.tsv'
slimbench_V1 elmpfam=FILE Download from ELM website of ELM Pfam domain interactors 'elm_interaction_domains.tsv'
slimbench_V1 pdbdata=FILE File mapping PDB identifiers onto genes/proteins
slimbench_V1 pfamdata=FILE File mapping PFam domains onto genes/proteins (BioMart or HMM search)
slimbench_V1 randsource=FILE Source for new sequences for random datasets None
slimbench_V1 uniprot=FILE File of downloaded UniProt entries (See rje_uniprot for more details) 'ELM.dat'
slimbench_V1 xrefdata=FILE File of gene identifier cross-reference data from rje_genemap
slimdip basefile=FILE Sets the basefile for all input/output. If not given, will use the ppifile=FILE base None
slimdip motifs=FILE File containing the SLiMs to analyse. (Required.) "ELM" will create/use ELM download. ELM
slimfarmer jobini=FILE Ini file to pass to the farmed SLiMSuite run. (Also used for SLiMFarmer options if qsub=T.) None
slimfarmer resfile=FILE Main output file for SLiMSuite run `farm`.csv
slimfarmer seqin=FILE Input sequence file to farm out None
slimfinder aadimerfreq=FILE Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) (!!!Experimental!!!) None
slimfinder focus=FILE FILE containing focal groups for SLiM return (see Manual for details) None
slimfinder gablamdis=FILE Alternative GABLAM results file None
slimfinder megaslim=FILE Make/use precomputed results for a proteome (FILE) in fasta format None
slimfinder resfile=FILE Main SLiMFinder results table slimfinder.csv
slimfinder_V4.9 aadimerfreq=FILE Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) (!!!Experimental!!!) None
slimfinder_V4.9 aafreq=FILE Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) None
slimfinder_V4.9 altdis=FILE Alternative all by all distance matrix for relationships None
slimfinder_V4.9 focus=FILE FILE containing focal groups for SLiM return (see Manual for details) None
slimfinder_V4.9 gablamdis=FILE Alternative GABLAM results file None
slimfinder_V4.9 negatives=FILE Multiply raw probabilities by under-representation in FILE (!!!Experimental!!!) None
slimfinder_V4.9 resfile=FILE Main SLiMFinder results table slimfinder.csv
slimfinder_V4.9 seqin=FILE Sequence file to search None
slimfinder_V4.9 slimcheck=FILE Motif file/list to add to resfile output
slimfrap domtable=FILE Table of domain predictions None
slimfrap elm=FILE File of ELM Motifs None
slimfrap nandr=FILE File of Neduva & Russell motifs None
slimfrap pairwise=FILE Pingu Pairwise PPI file None
slimfrap pickledata=FILE Genemap pickle to import and use. (See other rje_genemap options) None
slimgoer resfile=FILE Basefile for SLiMSearch results CSV files
slimjim pairwise=FILE Pingu Pairwise output file
slimjim resfile=FILE Main SLiMFinder results file
slimjim singlesf=FILE Path to *.slimdb file for which to generate graphics for single run
slimmutant dmifile=FILE Delimited text file containing domain-motif interaction data 'elm_interaction_domains.tsv'
slimmutant motifs=FILE Input file of SLiMs
slimmutant mutfile=FILE Delimited text file with sequence mutation info. Sets basefile.
slimmutant resfile=FILE Main SLiMProb results table (*.csv and *.occ.csv) slimprob.csv
slimmutant seqin=FILE Input file with protein sequences
slimparser restin=FILE Full REST output file, REST jobid (number), or full REST call URL (http://...)
slimpid ddi=FILE iPFam domain-domain interaction file
slimpid fam=FILE File of GABLAM results for family-based methods
slimpid ppi=FILE Pingu PPI File with Gene, EnsLoci & PPI headers
slimprob aadimerfreq=FILE Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) None
slimprob aafreq=FILE Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) None
slimprob altdis=FILE Alternative all by all distance matrix for relationships None
slimprob background=FILE Use observed support in background file for over-representation calculations None
slimprob gablamdis=FILE Alternative GABLAM results file None
slimprob megaslim=FILE Make/use precomputed results for a proteome (FILE) in fasta format None
slimprob motifs=FILE File of input motifs/peptides (also motif=X) None
slimprob negatives=FILE Multiply raw probabilities by under-representation in FILE None
slimprob resfile=FILE Main SLiMProb results table (*.csv and *.occ.csv) slimprob.csv
slimprob_V1.4 aadimerfreq=FILE Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) None
slimprob_V1.4 aafreq=FILE Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) None
slimprob_V1.4 altdis=FILE Alternative all by all distance matrix for relationships None
slimprob_V1.4 background=FILE Use observed support in background file for over-representation calculations None
slimprob_V1.4 gablamdis=FILE Alternative GABLAM results file None
slimprob_V1.4 motifs=FILE File of input motifs/peptides None
slimprob_V1.4 negatives=FILE Multiply raw probabilities by under-representation in FILE None
slimprob_V1.4 resfile=FILE Main SLiMProb results table (*.csv and *.occ.csv) slimprob.csv
slimprob_V1.4 seqin=FILE Sequence file to search None
slimsearch aadimerfreq=FILE Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) None
slimsearch aafreq=FILE Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) None
slimsearch altdis=FILE Alternative all by all distance matrix for relationships None
slimsearch background=FILE Use observed support in background file for over-representation calculations None
slimsearch gablamdis=FILE Alternative GABLAM results file None
slimsearch motifs=FILE File of input motifs/peptides None
slimsearch negatives=FILE Multiply raw probabilities by under-representation in FILE None
slimsearch resfile=FILE Main SLiMSearch results table slimsearch.csv
slimsearch seqin=FILE Sequence file to search None
smrtscape basefile=FILE Sets the root filename for all output, including the log smrtscape
smrtscape preassembly=FILE Preassembly fasta file for which to assess/correct over-fragmentation None
smrtscape seqin=FILE Subread sequence file for analysis (over-rides batch command) None
smrtscape_V1 preassembly=FILE Preassembly fasta file to assess/correct over-fragmentation (use seqin=FILE for subreads) None
smrtscape_V1 seqin=FILE Subread sequence file for analysis None
snapper basefile=FILE Root of output file names (same as SNP input file by default) or .vs.
snapper ftfile=FILE Input feature file (locus,feature,position,start,end) *.Feature.tdt
snapper reference=FILE Fasta (with accession numbers matching Locus IDs) or genbank file of reference genome.
snapper snpmap=FILE Input table of SNPs for standalone mapping and output (should have locus and pos info) None
snp_mapper basefile=FILE Root of output file names (same as SNP input file by default)
snp_mapper ftfile=FILE Input feature file (locus,feature,position,start,end) *.Feature.tdt
snp_mapper genbase=FILE Basefile for Genbank output. Will use base of seqin if None
snp_mapper seqin=FILE Sequence input file with accession numbers matching Locus IDs, or Genbank file.
snp_mapper snpfile=FILE Input table of SNPs to map and output (should have locus and pos info, see above)
trex basefile=FILE Root of output file names preassembly basefile
unifake aliases=FILE File of aliases to be added to Accession number list (for indexing) None
unifake datout=FILE Name of output DAT file Default input FILE.dat
unifake pfam=FILE PFam HMM download None
unifake seqin=FILE Input sequence file. See rje_seq documentation for filtering options. None
unifake signalp=FILE Path to SignalP program None
unifake tmhmm=FILE Path to TMHMM program None
wormpump outfile=FILE Name of output file wormpump.tdt

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