get.groups

The get.groups command selects sequences from a specific group or set of groups from the following file types: fasta, name, group, list, taxonomy. 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 > get.groups(group=abrecovery.groups, groups=B-C)

or

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

or

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

Both commands will output a new abrecovery.pick.groups containing the 158 sequences in groups B or C.

Options

fasta option

To use the fasta option, follow this example:

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

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

>AY457831
CCCTTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGCGCCTAACACATGCAAGTCGAACGAGCGAGAGGAGGTTTAC...
>AY457830
GCCCTTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGCGCCTAACACATGCAAGTCGAACGGAGCTTAGAGAGCTTG...
>AY457829
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCACTTTGATCGATT...
>AY457828
GCCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGGATCCATCAAGCTTG...
>AY457827
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCAGCATGGTCTTAGCT...
>AY457826
GCCCTTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGCGCCTAACACATGCAAGTCGAACGAGCGAGAGAGAGCTTG...
>AY457825
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCAGCATTTTAGTTTGC...
...

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 > get.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:

AY457721   AY457721
AY457733   AY457733
AY457723   AY457723
AY457741   AY457741
AY457686   AY457686
AY457758   AY457758
AY457693   AY457693
AY457706   AY457706
AY457674   AY457674
...

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

list option

To use the list option, follow this example:

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

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

unique 157 AY457741    AY457731    AY457682    AY457729    AY457734... 
0.00   152 AY457741    AY457731    AY457682    AY457729    AY457734...
0.01   105 AY457741    AY457731    AY457682    AY457729    AY457734... 
0.02   66  AY457741    AY457731    AY457682    AY457729    AY457734...
0.03   52  AY457741    AY457731    AY457682    AY457729    AY457734... 
...

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

taxonomy option

To use the taxonomy option, follow this example:

mothur > get.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:

AY457831   Bacteria(100);Firmicutes(100);Clostridiales(100);Ruminococcus_et_rel.(100);Anaerofilum-Faecalibacterium(100);...
AY457830   Bacteria(100);Firmicutes(100);Clostridiales(100);Ruminococcus_et_rel.(100);Anaerofilum-Faecalibacterium(100);...
AY457829   Bacteria(100);Firmicutes(100);Clostridiales(100);Johnsonella_et_rel.(100);Johnsonella_et_rel.(100);...
AY457828   Bacteria(100);Actinobacteria(100);Actinomycetaceae-Bifidobacteriaceae(100);Bifidobacteriaceae(100);...
AY457827   Bacteria(100);Bacteroidetes-Chlorobi(100);Bacteroidetes(100);Bacteroides-Prevotella(100);Bacteroides(100);...
AY457826   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 > get.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 Otu1    Otu2    Otu4    Otu5    Otu6    Otu7    Otu8    Otu12   Otu14   Otu15   Otu16   ... 
0.03   B   52  0   0   0   0   0   1   1   8   1   7   1   ... 
0.03   C   52  1   1   1   1   1   0   0   0   7   0   1   ...

You can see that some OTU’s were entirely eliminated because they only contained sequences from group A.

design

To use the design option, follow this example:

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

sets

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

Revisions