split.groups

The split.groups command reads a list, fasta, flow or fastq file and count and generates a list, fasta, flow or fastq files for each group in the count file. To run through the example below, download Example Data

Default Settings

The count is required.

mothur > split.groups(fasta=final.fasta, count=final.count_table)

This command generates 18 files.

final.F3D0.count_table
final.F3D0.fasta
final.F3D1.count_table
final.F3D1.fasta
final.F3D141.count_table
final.F3D141.fasta
final.F3D142.count_table
final.F3D142.fasta
final.F3D143.count_table
final.F3D143.fasta
final.F3D144.count_table
final.F3D144.fasta
final.F3D145.count_table
final.F3D145.fasta
final.F3D146.count_table
final.F3D146.fasta
final.F3D147.count_table
final.F3D147.fasta
final.F3D148.count_table
final.F3D148.fasta
final.F3D149.count_table
final.F3D149.fasta
final.F3D150.count_table
final.F3D150.fasta
final.F3D2.count_table
final.F3D2.fasta
final.F3D3.count_table
final.F3D3.fasta
final.F3D5.count_table
final.F3D5.fasta
final.F3D6.count_table
final.F3D6.fasta
final.F3D7.count_table
final.F3D7.fasta
final.F3D8.count_table
final.F3D8.fasta
final.F3D9.count_table
final.F3D9.fasta

Options

groups

The groups parameter allows you to select groups to create files for. For example if you set groups=F3D0-F3D1-F3D2, you will 6 output files.

mothur > split.groups(fasta=final.fasta, count=final.count_table, groups=F3D0-F3D1-F3D2)

final.F3D0.count_table
final.F3D0.fasta
final.F3D1.count_table
final.F3D1.fasta
final.F3D2.count_table
final.F3D2.fasta

flow

The flow parameter is used to input your flow file.

fastq

The flow parameter is used to input your fastq file.

processors

The processors option enables you to accelerate the parsing by using multiple processors. Default processors=Autodetect number of available processors and use all available.

The name option allows you to provide a name file associated with your group file.

We DO NOT recommend using the name file. Instead we recommend using a count file. The count file reduces the time and resources needed to process commands. It is a smaller file and can contain group information.

The group parameter allows you to provide a group file to use when selecting items from your files.

We DO NOT recommend using the name / group file combination. Instead we recommend using a count file. The count file reduces the time and resources needed to process commands. It is a smaller file and can contain group information.

Revisions

  • 1.28.0 - Added count parameter
  • 1.32.0 - Bug Fix: not splitting properly with a count file.
  • 1.40.0 - Adds flow parameter.
  • 1.42.0 - Adds fastq parameter. #499
  • 1.43.0 - Adds list parameter. #624
  • 1.44.0 - Adds processors parameter. #685
  • 1.47.0 - Fixes crash with split.groups when running with fasta and group files without a names file. Effects allfiles options in other commands.
  • 1.48.0 Fixes bug with split.groups flow file option with count table