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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


ModuleOptionDescriptionDefault
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

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