fasta_write: Write a fasta file with the taxonomy
In vaulot/dvutils: A set of utilities
Description
Usage
Arguments
Examples
Description
Write a fasta file from a set of sequences
Option : add to the definition line the the taxonomy separated by separator character (e.g. |)Otu0001|Alveolata|Dinophyta|Syndiniales|Dino-Group-I|Dino-Group-I-Clade-1|Dino-Group-I-Clade-1_X|Dino-Group-I-Clade-1_X_sp.
AGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGGA...
Usage
1
2
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fasta_write(
df,
file_name,
compress = FALSE,
taxo_include = TRUE,
taxo_separator = "|"
)
Arguments
df
The data frame with the otu names, the taxonomy and the sequences. It should have the following columns (with exactly these names)
* seq_name : the sequence name
* supergroup: species
* sequence
file_name
Character, where to save the fasta file
compress
If TRUE produces a gz file
taxo_include
If TRUE then add taxo information which must be provided
taxo_separator
Character used to separate the different taxonomic levels
TRUE if it terminates OK
Examples
1
fasta_write(df,"otu_taxo.fasta", compress=FALSE, include_taxo=TRUE, taxo_separator=";")
vaulot/dvutils documentation built on Nov. 20, 2021, 11:01 a.m.
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Description Usage Arguments Examples
Description
Write a fasta file from a set of sequences Option : add to the definition line the the taxonomy separated by separator character (e.g. |)Otu0001|Alveolata|Dinophyta|Syndiniales|Dino-Group-I|Dino-Group-I-Clade-1|Dino-Group-I-Clade-1_X|Dino-Group-I-Clade-1_X_sp.
AGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGGA...
Usage
1 2 3 4 5 6 7 | fasta_write(
df,
file_name,
compress = FALSE,
taxo_include = TRUE,
taxo_separator = "|"
)
|
Arguments
df |
The data frame with the otu names, the taxonomy and the sequences. It should have the following columns (with exactly these names) * seq_name : the sequence name * supergroup: species * sequence |
file_name |
Character, where to save the fasta file |
compress |
If TRUE produces a gz file |
taxo_include |
If TRUE then add taxo information which must be provided |
taxo_separator |
Character used to separate the different taxonomic levels TRUE if it terminates OK |
Examples
1 | fasta_write(df,"otu_taxo.fasta", compress=FALSE, include_taxo=TRUE, taxo_separator=";")
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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