make.count
The make.count command reads a file, fasta file or series of fasta files and creates a count file.
Default Options
fasta && groups
mothur > make.count(fasta=sample1.fasta-sample2.fasta, groups=A-B)
Assigning sequences from file sample1.fasta to group A: 10 sequences assigned to group A
Assigning sequences from file sample2.fasta to group B: 1 sequences assigned to group B
Group count:
A 10
B 1
Total of all groups is 11
Output File Names: merge.count_table
This command creates a file called merge.count_table.
Options
file
The file parameter allows you to associate fasta files to sample names. mothur can create this for you with the make.file command.
mothur > make.file(inputdir=./fasta, type=fasta)
The resulting stability.files will look like:
testfile.DN1576.CAD testfile.DN1576.CAD_705.fasta
testfile.DN1576.EF1a testfile.DN1576.EF1a_771.fasta
testfile.DN1576.MDH testfile.DN1576.MDH_498.fasta
testfile.DN1576.RpS5 testfile.DN1576.RpS5_597.fasta
testfile.DN1577.EF1a testfile.DN1577.EF1a_771.fasta
testfile.DN1577.MDH testfile.DN1577.MDH_498.fasta
testfile.DN1577.RpS5 testfile.DN1577.RpS5_597.fasta
testfile.DN1578.CAD testfile.DN1578.CAD_705.fasta
testfile.DN1578.EF1a testfile.DN1578.EF1a_771.fasta
...
With the stability.files as input:
mothur > make.count(file=stability.files)
This command creates a file called stability.count_table.
output
The output parameter allows you to specify the name of count file created.
mothur > make.count(fasta=sample1.fasta-sample2.fasta, groups=A-B, output=samples.count_table)
format
The format parameter allows you to specify whether the outputted file is a group file or count file. Options group or count. Default=count.
Revisions
- 1.48.0 First Introduced
- 1.48.1 Adds file option