set.current

The set.current command allows you to set.current files for mothur to use. You can also clear current files.

Default Options

Let’s set a current fasta and name file and then see how mothur will use them. NOTE: For REQUIRED parameters if you do not provide the file mothur will automatically check to see if there is a current file of that type.

mothur > set.current(fasta=stool.fasta, name=stool.names)

Current files saved by mothur:
fasta=/Users/SarahsWork/Desktop/release/stool.fasta
name=/Users/SarahsWork/Desktop/release/stool.names

mothur > summary.seqs()
Using stool.fasta as input file for the fasta parameter.

       Start   End NBases  Ambigs  Polymer
Minimum:   1   183 183 0   3
2.5%-tile: 1   243 243 0   4
25%-tile:  1   259 259 0   5
Median:    1   267 267 0   5
75%-tile:  1   274 274 0   5
97.5%-tile:    1   287 287 0   6
Maximum:   1   373 373 0   6
# of Seqs: 37126

Output File Name: 
stool.fasta.summary

Since the fasta parameter is required for the summary.seqs command mothur will use the current fasta file. Now see what happens with unique.seqs.

mothur > set.current(fasta=stool.fasta, name=stool.names)
mothur > unique.seqs()
Using stool.fasta as input file for the fasta parameter.

Output File Names: 
stool.unique.fasta
stool.names

If you want to use the name file, you must set name=current since the name parameter is not required.

mothur > set.current(fasta=stool.fasta, name=stool.names)
mothur > unique.seqs(name=current)
Using stool.names as input file for the name parameter.
Using stool.fasta as input file for the fasta parameter.

Output File Names: 
stool.unique.fasta
stool.names

clear

You can clear specific file values by separating their names with dashes.

mothur > summary.seqs(fasta=stool.fasta)
mothur > unique.seqs(fasta=stool.fasta)
mothur > set.current(clear=fasta)

Current files saved by mothur:
name=/Users/SarahsWork/Desktop/release/stool.names

or you can clear all files by setting clear=all.

mothur > summary.seqs(fasta=stool.fasta)
mothur > unique.seqs(fasta=stool.fasta)
mothur > set.current(clear=all)

Current files saved by mothur:

current

The current parameter can be used to input the output file from get.current. This allows the commands to work together to keep track of current files between instances of mothur.

Revisions

  • 1.33.0 - Bug Fix: setting processors option to 1, if not set.
  • 1.37.0 - Adds current parameter.