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SLiMSuite Documentation

Please note that command documentation sometimes lags behind the latest module versions. Click on module names to check current documentation.

cmd: basefile

Option Type: [?]{docs:?} FILE X

Modules: diploidocus extatic jrj_fastq patis prothunter revert rje_archive rje_paml rje_taxamap samphaser slimdip spydarm trex rje_genbank rje_genemap rje_hpc rje_iridis rje_obj rje_samtools rje_synteny rje_taxonomy rje_uniprot rje rje_xref snp_mapper aphid badasp budapest gfessa haqesac pagsat_V1 pagsat picsi pingu_V3 pingu_V4 seqmapper slimfarmer smrtscape snapper

Module	Option	Description	Default
aphid	`basefile=X`	Text base for output files and resdir	`default based on data file name`
badasp	`basefile=X`	Basic 'root' for all files X.*	`By default will use 'root' of seqin=FILE if given or haq_AccNum if qblast`
budapest	`basefile=X`	"Base" name for all results files, e.g. X.budapest.tdt	`MASCOT file basename`
diploidocus	`basefile=FILE`	Root of output file names	`diploidocus`
extatic	`basefile=X`	Root name for output files. Path will be stripped and resdir used.	`* based on cdna or singleseq`
gfessa	`basefile=X`	"Base" name for all results files, e.g. X.gfessa.tdt	`TAG file basename`
haqesac	`basefile=X`	Basic 'root' for all files X.*	`By default will use 'root' of seqin=FILE if given or haq_AccNum if qblast`
jrj_fastq	`basefile=FILE`	Base name for output (input by default)	`None`
pagsat	`basefile=X`	Basename for output files and directories.	`assembly+ref`
pagsat_V1	`basefile=X`	Basename for output files and directories.	`assembly+ref`
patis	`basefile=X`	Leader for .utr5.fas and .cds.fas sequences - should start with species	`Homo_sapiens.GRCh37.p13`
picsi	`basefile=FILE`	Base for output files	`picsi`
pingu_V3	`basefile=X`	Results file prefix if no data file given with data=FILE	`pingu`
pingu_V4	`basefile=X`	Results file prefix	`pingu`
prothunter	`basefile=X`	This will control output file names and also be used to pick up later analyses for HTML etc.
revert	`basefile=FILE`	Root of output files. Defaults to `virusgb.genome` if blank/None	`None`
rje	`[basefile=?]{docs:?}`		`?`
rje_archive	`basefile=FILE`	This will set the 'root' filename for output files (FILE.*), including the log	`'rds'`
rje_genbank	`basefile=FILE`	Root of output file names (same as input file by default)
rje_genemap	`basefile=X`	Root for output files	`genemap`
rje_hpc	`basefile=X`	Base for output files - compiled from individual run results	`None`
rje_iridis	`basefile=X`	Base for output files - compiled from individual run results	`None`
rje_obj	`[basefile=?]{docs:?}`		`?`
rje_paml	`basefile=X`	Base for names of results files	`'pamlres'`
rje_samtools	`basefile=X`	Basename for frequency comparison output	`.v.`
rje_synteny	`basefile=FILE`	Basename for output files	`ftgablam basefile`
rje_taxamap	`basefile=X`	Base for output files. Will reuse unless force=T	`'taxmap'`
rje_taxonomy	`basefile=X`	Results file prefix. Will use first taxin=LIST term if missing	`None`
rje_uniprot	`basefile=X`	If set, can use "T" or "True" for other `*out` options. (Will default to `datout` if given)	`None`
rje_xref	`basefile=X`	Basefile for output files	`Default: filexref or first xrefdata input file w/o path`
samphaser	`basefile=FILE`	Root of output file names (same as Pileup input file by default)
seqmapper	`basefile=FILE`	Set resfile=FILE and log=FILE at the same time
slimdip	`basefile=FILE`	Sets the basefile for all input/output. If not given, will use the ppifile=FILE base	`None`
slimfarmer	`basefile=X`	Set the log, RunID, ResFile, ResDir and Job to X	`None`
smrtscape	`basefile=FILE`	Sets the root filename for all output, including the log	`smrtscape`
snapper	`basefile=FILE`	Root of output file names (same as SNP input file by default)	`or .vs.`
snp_mapper	`basefile=FILE`	Root of output file names (same as SNP input file by default)
spydarm	`basefile=X`	Prefix for output files	`slimsuite`
trex	`basefile=FILE`	Root of output file names	`preassembly basefile`