Module | Option | Description | Default |
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 |