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Difference between revisions of "Remove.groups"
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* 1.37.0 Adds phylip and column options [https://github.com/mothur/mothur/issues/79 #79] | * 1.37.0 Adds phylip and column options [https://github.com/mothur/mothur/issues/79 #79] | ||
* 1.40.0 - Speed and memory improvements for shared files. [https://github.com/mothur/mothur/issues/357 #357] , [https://github.com/mothur/mothur/issues/347 #347] | * 1.40.0 - Speed and memory improvements for shared files. [https://github.com/mothur/mothur/issues/357 #357] , [https://github.com/mothur/mothur/issues/347 #347] | ||
| + | * 1.40.0 - Allow for () characters in taxonomy definitions. [https://github.com/mothur/mothur/issues/350 #350] | ||
[[Category:Commands]] | [[Category:Commands]] | ||
Latest revision as of 14:57, 29 March 2018
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.
Contents
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.
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 > 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.
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.
- 1.37.0 Adds phylip and column options #79
- 1.40.0 - Speed and memory improvements for shared files. #357 , #347
- 1.40.0 - Allow for () characters in taxonomy definitions. #350
