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Get.current

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The get.current command allows you to find out which files mothur has saved as "current" for each type. You can also clear current files.

Default Options

First let's get some current files saved.

mothur > summary.seqs(fasta=stool.fasta)
mothur > unique.seqs(fasta=stool.fasta)

Now we can see how the get.current command works.

mothur > get.current()

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

You can also use these current files to help with mothur's long file names.

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

Screen Output:

mothur > summary.seqs(fasta=stool.fasta)

		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


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

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

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. So in the above example you could also run unique.seqs without providing a fasta file name.

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 > get.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 > get.current(clear=all)

Current files saved by mothur:


Revisions

  • 1.33.0 - added directory information. - http://www.mothur.org/forum/viewtopic.php?f=8&t=332&p=7824#p7824
  • 1.37.0 - Adds current RAM usage and total RAM available.
  • 1.37.0 - Adds output file to get.current and input/output file to set.current . This allows the commands to work together to keep track of current files between instances of mothur. You can input the output file of the get.current command into the set.current command using the new current parameter.
  • 1.38.0 - Fixes RAM output for linux.