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Difference between revisions of "Get.sharedseqs"

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The '''get.sharedotu''' command takes a list and group file and outputs a list of sequences in the otus shared by all groups. You can use the groups parameter to see the shared otus by specific groups, and the label parameter to specify the distance you are interested in. You can also input a fasta file and mothur will generate a fasta file containing only the sequences in these shared otus.
+
The '''get.sharedotu''' command takes a list and group file and outputs a .names file for each distance.   To run through the commands below use [[Media:AbRecovery2.zip | AbRecovery files]].
  
Until more documentation is available, please consult the in-program help:
 
  
  mothur > get.sharedotu(help)
+
__TOC__
 +
 
 +
 
 +
==Default settings==
 +
To execute the get.sharedotu() command you must provide a list and group file.  By default this will output the otus shared by all the groups in your groupfile. For example:
 +
 
 +
  mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups)
 +
 
 +
This will result in output to the screen looking like:
 +
 
 +
unique 0 - No otus shared by groups  A  B  C.
 +
0.00 0 - No otus shared by groups  A  B  C.
 +
0.01 1
 +
0.02 2
 +
0.03 3
 +
0.04 3
 +
0.05 4
 +
0.06 5
 +
0.07 6
 +
...
 +
 
 +
 
 +
The left column indicates the label for each line in the data set and the right column indicates the number of OTUs at this distance. 
 +
 
 +
The .name output files look like:  name|group|bin#
 
   
 
   
  The get.sharedotu command parameters are list, group, label, groups, output and fasta. The list and group parameters are required.
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  AY457715|C|59
  The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.
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AY457838|A|59
  The groups parameter allows you to select groups you would like to know the shared info for, and are separated by dashes.
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AY457774|B|59
  The fasta parameter allows you to input a fasta file and outputs a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified.
+
 
  The output parameter allows you to output the list of names without the group and bin number added.  
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==Options==
With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos.   
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The get.sharedotu command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.
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===fasta===
  The get.sharedotu command should be in the following format: get.sabund(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).
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If you provide a fasta file mothur will also output a fasta file for each distance you specify:
Example get.sharedotu(label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).
+
 
The default value for label is all labels in your inputfile. The default for groups is all groups in your file.
+
mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups, fasta=abrecovery.fasta)
 +
 
 +
The .fasta output files look like:
 +
 
 +
>AY457838|A|59
 +
CCCTTAGAGTTTGATCCTGGCTCAGGACG...
 +
>AY457774|B|59
 +
CCCTTAGAGTTTGATCCTGGCTCAGGACG...
 +
>AY457715|C|59
 +
CCCTTAGAGTTTGATCCTGGCTCAGGACG...
 +
 
 +
 
 +
===label===
 +
There may only be a couple of lines in your list file that you are interested in. There are two options.  You could: (i) manually delete the lines you aren't interested in from you list file; (ii) or use the label option. 
 +
 
 +
  mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups, label=0.04-0.82)
 +
0.04 3
 +
0.82 1
 +
 
 +
 
 +
Opening abrecovery.fn.0.04.names you would see the output as:
 +
 
 +
  AY457701|C|45
 +
AY457715|C|45
 +
AY457838|A|45
 +
AY457774|B|45
 +
AY457747|C|45
 +
AY457859|A|45
 +
AY457695|C|46
 +
AY457732|C|46
 +
AY457860|A|46
 +
AY457826|B|46
 +
AY457767|B|46
 +
AY457698|C|111
 +
AY457855|A|111
 +
AY457804|B|111
 +
 
 +
===groups===
 +
The groups parameter allows you to see otus shared by specific groups or unique to a particular group.  For example to see the otus at distance 0.04 unique to group A, you would enter the following:
 +
 
 +
mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups, label=0.04, groups=A)
 +
  0.04 38
 +
 
 +
There are 38 otus unique to A at distance 0.04 and their names are listed in abrecovery.fn.0.04.names.
 +
   
 +
 
 +
===output===
 +
The output parameter allows you to have the .names file be in .accnos form so you can use it with the [[get.seqs]], [[list.seqs]] and [[remove.seqs]] commands.  For example:
 +
 
 +
  mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups, label=0.04, output=accnos)
 +
 
 +
Opening abrecovery.fn.0.04.names you would see the output as:
  
[[Category:Commands]]
+
AY457701
 +
AY457715
 +
AY457838
 +
AY457774
 +
AY457747
 +
AY457859
 +
AY457695
 +
AY457732
 +
AY457860
 +
AY457826
 +
AY457767
 +
AY457698
 +
AY457855
 +
AY457804

Revision as of 20:46, 23 November 2009

The get.sharedotu command takes a list and group file and outputs a .names file for each distance. To run through the commands below use AbRecovery files.



Default settings

To execute the get.sharedotu() command you must provide a list and group file. By default this will output the otus shared by all the groups in your groupfile. For example:

mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups)

This will result in output to the screen looking like:

unique	0 - No otus shared by groups  A  B  C.
0.00	0 - No otus shared by groups  A  B  C.
0.01	1
0.02	2
0.03	3
0.04	3
0.05	4
0.06	5
0.07	6
...


The left column indicates the label for each line in the data set and the right column indicates the number of OTUs at this distance.

The .name output files look like: name|group|bin#

AY457715|C|59
AY457838|A|59
AY457774|B|59

Options

fasta

If you provide a fasta file mothur will also output a fasta file for each distance you specify:

mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups, fasta=abrecovery.fasta)

The .fasta output files look like:

>AY457838|A|59
CCCTTAGAGTTTGATCCTGGCTCAGGACG...
>AY457774|B|59
CCCTTAGAGTTTGATCCTGGCTCAGGACG...
>AY457715|C|59
CCCTTAGAGTTTGATCCTGGCTCAGGACG...


label

There may only be a couple of lines in your list file that you are interested in. There are two options. You could: (i) manually delete the lines you aren't interested in from you list file; (ii) or use the label option.

mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups, label=0.04-0.82)
0.04	3
0.82	1


Opening abrecovery.fn.0.04.names you would see the output as:

AY457701|C|45
AY457715|C|45
AY457838|A|45
AY457774|B|45
AY457747|C|45
AY457859|A|45
AY457695|C|46
AY457732|C|46
AY457860|A|46
AY457826|B|46
AY457767|B|46
AY457698|C|111
AY457855|A|111
AY457804|B|111

groups

The groups parameter allows you to see otus shared by specific groups or unique to a particular group. For example to see the otus at distance 0.04 unique to group A, you would enter the following:

mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups, label=0.04, groups=A)
0.04	38

There are 38 otus unique to A at distance 0.04 and their names are listed in abrecovery.fn.0.04.names.


output

The output parameter allows you to have the .names file be in .accnos form so you can use it with the get.seqs, list.seqs and remove.seqs commands. For example:

mothur > get.sharedotu(list=abrecovery.fn.list, group=abrecovery.groups, label=0.04, output=accnos)

Opening abrecovery.fn.0.04.names you would see the output as:

AY457701
AY457715
AY457838
AY457774
AY457747
AY457859
AY457695
AY457732
AY457860
AY457826
AY457767
AY457698
AY457855
AY457804