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Rename.file

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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