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Get.groups

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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)

Revisions