remove.groups

The remove.groups command removes sequences from a specific group or set of groups from the following file types: fasta, name, group, list, taxonomy and shared. To complete this analysis, you need to download the folder compressed in the Abrecovery.zip and Abrecovery.accnosgroups.zip.

Default Settings

The group or count parameter is required, unless you have a current group or count file, or are using a shared file. The command will generate a *.pick.* file.

mothur > remove.groups(group=abrecovery.groups, groups=B-C)

or with a count file:

mothur > remove.groups(count=abrecovery.count_table, groups=B-C)

or you may wish to list your groups in a file instead of manually typing them. This can be done by using an accnos file.

mothur > remove.groups(group=abrecovery.groups, accnos=abrecovery.accnosgroups) 

or with a count file:

mothur > remove.groups(count=abrecovery.count_table, accnos=abrecovery.accnosgroups) 

Both commands will output a new abrecovery.pick.groups containing the 84 sequences not in groups B or C.

Options

fasta option

To use the fasta option, follow this example:

mothur > remove.groups(group=abrecovery.groups, groups=B-C, fasta=abrecovery.fasta)

This generates the file abrecovery.pick.fasta, which contains the following lines:

>AY457915
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCATTTAAG...
>AY457914
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCATTTAGAA...
>AY457913
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCACTTTTAC...
>AY457912
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCATTTGCGA...
>AY457911
CCCTTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGCGCCTAACACATGCAAGTCGAACGAGCGAGAGAGAG...
>AY457910
CCCTTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGCGCCTAACACATGCAAGTCGAACGAGAGAGAGGGAG...
>AY457909
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCAGCATGGTCT...
...

as well as a abrecovery.pick.groups with the same sequences.

phylip

The phylip option is used to specify the name of the phylip formatted distance file you would like to select distances from.

The final.tre1.weighted.ave.dist file contains:

11
F003D000   
F003D002   0.219014    
F003D004   0.405823    0.285439    
F003D006   0.311126    0.227599    0.197012    
F003D008   0.246074    0.221351    0.341801    0.220774    
F003D142   0.381307    0.350587    0.175825    0.199702    0.331989    
F003D144   0.380843    0.3943  0.350766    0.278915    0.37678 0.239005    
F003D146   0.277258    0.300362    0.331904    0.242542    0.239576    0.246918    0.160718    
F003D148   0.308621    0.299937    0.303805    0.254025    0.27361 0.246377    0.15778 0.120112    
F003D150   0.315133    0.307792    0.206429    0.209389    0.27078 0.179998    0.260263    0.217917    0.195339    
MOCK.GQY1XT001 0.64778 0.69245 0.769817    0.703035    0.61892 0.715547    0.662322    0.613735    0.648762    0.716918    

mothur > get.dists(phylip=final.tre1.weighted.ave.dist, accnos=final.test.accnos)

creates a final.tre1.weighted.ave.pick.dist file:

5
F003D000   
F003D002   0.219014    
F003D004   0.405823    0.285439    
F003D142   0.381307    0.350587    0.175825    
F003D144   0.380843    0.3943  0.350766    0.239005    

column

The column option is used to specify the name of the column formatted distance file you would like to select distances from.

U68590 U68589 0.67
U68591 U68589 0.7559
U68591 U68590 0.8011
U68592 U68589 0.6585
U68592 U68590 0.6528
U68592 U68591 0.7849
U68593 U68589 0.6953
U68593 U68590 0.6383
U68593 U68591 0.7741
U68593 U68592 0.6041
U68594 U68589 0.7109
U68594 U68590 0.7233
...

If you only want sequences U68589, U68590 and U68592.

mothur > get.dists(column=amazon.dist, accnos=amazon.test.accnos)

amazon.pick.dist contains:

U68590 U68589  0.67
U68592 U68589  0.6585
U68592 U68590  0.6528

name option

To use the name option, follow this example:

mothur > remove.groups(fasta=abrecovery.fasta, group=abrecovery.groups, groups=B-C, name=abrecovery.names)

This generates the file abrecovery.pick.names, which contains the following lines:

AY457841   AY457841
AY457869   AY457869
AY457846   AY457846
AY457875   AY457875
AY457865   AY457865
AY457855   AY457855
...

as well as a abrecovery.pick.groups with the same sequences.

list option

To use the list option, follow this example:

mothur > remove.groups(group=abrecovery.groups, groups=B-C, list=abrecovery.fn.list)

or with a count file:

mothur > remove.groups(count=abrecovery.count_table, groups=B-C, list=abrecovery.fn.unique_list)

This generates the file abrecovery.fn.pick.list, which contains the following lines:

unique 84  AY457876    AY457841    AY457869    AY457875    AY45787 ... 
0.00   78  AY457876    AY457841    AY457869    AY457875    AY457871 ...    
0.01   56  AY457876    AY457841    AY457869    AY457875    AY457871 ...
0.02   45  AY457876    AY457841    AY457895,AY457912,AY457869  AY457875 ...    
...

as well as a abrecovery.pick.groups with the same sequences.

taxonomy option

To use the taxonomy option, follow this example:

mothur > remove.groups(group=abrecovery.groups, groups=B-C, taxonomy=abrecovery.silva.full.taxonomy)

This generates the file abrecovery.silva.full.pick.taxonomy, which contains the following lines:

AY457915   Bacteria(100);Firmicutes(100);Clostridiales(100);Johnsonella_et_rel.(100);Johnsonella_et_rel.(100);...
AY457914   Bacteria(100);Firmicutes(100);Clostridiales(100);Johnsonella_et_rel.(100);Johnsonella_et_rel.(100);...
AY457913   Bacteria(100);Firmicutes(100);Clostridiales(100);Johnsonella_et_rel.(100);Johnsonella_et_rel.(100);...
AY457912   Bacteria(100);Firmicutes(100);Clostridiales(100);Johnsonella_et_rel.(100);Johnsonella_et_rel.(100);...
AY457911   Bacteria(100);Firmicutes(100);Clostridiales(100);Ruminococcus_et_rel.(100);Anaerofilum-Faecalibacterium(100);...
AY457910   Bacteria(100);Firmicutes(100);Clostridiales(100);Ruminococcus_et_rel.(100);Anaerofilum-Faecalibacterium(100);...
...

as well as a abrecovery.pick.groups with the same sequences.

shared option

To use the shared option, follow this example:

mothur > remove.groups(shared=abrecovery.fn.shared, groups=B-C)

This generates the file abrecovery.fn.0.03.pick.shared, which contains the following lines:

label  Group   numOtus Otu3    Otu9    Otu10   Otu11   Otu12   Otu13   Otu14   Otu15   Otu16   Otu18   Otu19 ...   
0.03   A   36  1   1   5   1   1   4   2   5   1   1   1   ...

You can see that some OTUs were entirely eliminated because they only contained sequences from groups B and C.

design

The design parameter allows you to assign groups to treatments. You can use the design file with sets to remove all groups associated with a treatment. To use the design option, follow this example:

mothur > remove.groups(shared=abrecovery.shared, design=abrecovery.design, sets=B-C)

sets

The sets parameter allows you to specify which of the sets in your designfile you would like to remove. You can separate set names with dashes.

Revisions

1.23.0 File mismatch bug - https://forum.mothur.org/viewtopic.php?f=4&t=1396&p=3560#p3560
1.24.0 Added design option
1.28.0 Added count option
1.31.0 Bug Fix: remove.groups(groups=notValidGroupName, ...) mothur removes all of the groups. Fix will ignore invalid group and continue.
1.36.0 Bug Fix: not creating a list file for each label.
1.37.0 Adds phylip and column options #79
1.40.0 - Speed and memory improvements for shared files. #357 , #347
1.40.0 - Allow for () characters in taxonomy definitions. #350
1.44.0 - Adds sets parameter. #277