write.fasta

A named character vector where names are sequence names and
values are the sequences. Also accepts a <code>BIOM</code>
object which contains sequences.

seqs

Path to the output fasta file. Files ending in <code>.gz</code> or
<code>.bz2</code> will be compressed accordingly.

outfile

Write sequences from a BIOM object to a file in fasta format.

A toolkit for working with Biological Observation Matrix ('BIOM') files.
Features include reading/writing all 'BIOM' formats, rarefaction, alpha
diversity, beta diversity (including 'UniFrac'), summarizing counts by
taxonomic level, and sample subsetting. Standalone functions for
reading, writing, and subsetting phylogenetic trees are also provided.
All CPU intensive operations are encoded in C with multi-thread support.

Daniel P. Smith

rbiom

Read/Write, Transform, and Summarize 'BIOM' Data

write.fasta function

<dl><dt>seqs</dt>
<dd>A named character vector where names are sequence names and
values are the sequences. Also accepts a <code>BIOM</code>
object which contains sequences.</dd>
<dt>outfile</dt>
<dd>Path to the output fasta file. Files ending in <code>.gz</code> or
<code>.bz2</code> will be compressed accordingly.</dd></dl>

Arguments

Write sequences from a BIOM object to a file in fasta format. — write.fasta

<dl>

<dt>seqs</dt>
<dd>A named character vector where names are sequence names and
values are the sequences. Also accepts a <code>BIOM</code>
object which contains sequences.</dd>


<dt>outfile</dt>
<dd>Path to the output fasta file. Files ending in <code>.gz</code> or
<code>.bz2</code> will be compressed accordingly.</dd>

</dl>

write.fasta: Write sequences from a BIOM object to a file in fasta format.

Description

Usage

Value

Arguments