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Difference between revisions of "Remove.groups"

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(Created page with 'The remove.groups command removes sequences from a specific group or set of groups from the following file types: fasta, name, group, list, taxonomy. To complete this analysi...')
 
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The [[remove.groups]] command removes 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 [[Media:Abrecovery.zip | Abrecovery.zip]] and [[Media:Abrecovery.accnosgroups.zip | Abrecovery.accnosgroups.zip]].
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The [[remove.groups]] command removes 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 [[Media:AbRecovery.zip | Abrecovery.zip]] and [[Media:Abrecovery.accnosgroups.zip | Abrecovery.accnosgroups.zip]].
  
 
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Revision as of 20:27, 8 December 2010

The remove.groups command removes 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 parameter is required. The command will generate a *.pick.* file.

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

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 esophagus.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(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)

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.