We will be offering mothur and R workshops throughout 2019. Learn more.

Difference between revisions of "Remove.groups"

From mothur
Jump to: navigation, search
(Revisions)
(Revisions)
Line 127: Line 127:
 
* 1.28.0 Added count 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.  
 
* 1.31.0 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.
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Revision as of 21:09, 15 July 2015

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.

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

To use the design option, follow this example:

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

Revisions

  • 1.23.0 File mismatch bug - http://www.mothur.org/forum/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.