rename.file
The rename.file command allows you to rename.file from within mothur. mothur will update the current files saved by mothur as well.
Default Settings
The rename.file command parameters are: phylip, column, list, rabund, sabund, name, group, design, tree, shared, relabund, fasta, qfile, sff, oligos, accnos, biom, count, summary, file, taxonomy, constaxonomy, input, output, prefix, deletedold and shorten.
mothur > rename.file(fasta=current, name=current, group=current, taxonomy=current, prefix=final)
Current files saved by mothur:
fasta=final.fasta
name=final.names
group=final.groups
taxonomy=final.taxonomy
input
The input parameter allows you to provide an non typed input file name to be renamed.
mothur > rename.file(input=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.shared, new=final.an.shared)
Note: mothur will not save this file as the current shared file unless you use the shared parameter as the input.
new
The new parameter allows you to provide an output file name for the input file you provide.
prefix
The prefix parameter allows you to enter your own prefix for shortened names.
mothur > rename.file(shared=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.shared, prefix=final)
Current files saved by mothur:
shared=final.an.shared
shorten
The shorten parameter is used to inicate you want mothur to generate output file names for you. Default=true.
mothur > rename.file(shared=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.an.unique_list.shared)
Current files saved by mothur:
shared=stability.an.shared
deleteold
The deleteold parameter indicates whether you want to delete the old file. Default=true.
File Type Options
Using the file type options will cause mothur to update the current files saved by mothur.
phylip
You can enter you phylip file using the phylip parameter.
column
You can enter you column file using the column parameter.
list
You can enter you list file using the list parameter.
rabund
You can enter you rabund file using the rabund parameter.
sabund
You can enter you sabund file using the sabund parameter.
name
You can enter you name file using the name parameter.
group
You can enter you group file using the group parameter.
design
You can enter you design file using the design parameter.
tree
You can enter you tree file using the tree parameter.
shared
You can enter you shared file using the shared parameter.
relabund
You can enter you relabund file using the relabund parameter.
fasta
You can enter you fasta file using the fasta parameter.
qfile
You can enter you qfile file using the qfile parameter.
sff
You can enter you sff file using the sff parameter.
oligos
You can enter you oligos file using the oligos parameter.
accnos
You can enter you accnos file using the accnos parameter.
biom
You can enter you biom file using the biom parameter.
count
You can enter you count file using the count parameter.
summary
You can enter you summary file using the summary parameter.
file
You can enter you file file using the file parameter.
taxonomy
You can enter you taxonomy file using the taxonomy parameter.
constaxonomy
You can enter you constaxonomy file using the constaxonomy parameter.
Revisions
- 1.38.0 First Introduced
- 1.39.1 Fixes Bug allowing an automatically rename with output directory specified