parse_seq_input

(<code>character</code>) One of the following:<dl class="dl-horizontal">
 <dt>A character vector of sequences</dt><dd>See the example below for what this
 looks like. The parser <code><a rd-options="" href="/link/read_fasta?package=metacoder&version=0.2.0" data-mini-rdoc="metacoder::read_fasta">read_fasta</a></code> produces output like this.</dd>
 <dt>A list of character vectors</dt><dd>Each vector should have one base per element.</dd>
 <dt>A "DNAbin" object</dt><dd>This is the result of parsers like
 <code><a rd-options="ape" href="/link/read.FASTA?package=metacoder&version=0.2.0&to=ape" data-mini-rdoc="ape::read.FASTA">read.FASTA</a></code>.</dd>
 <dt>A list of "SeqFastadna" objects</dt><dd>This is the result of parsers like
 <code><a rd-options="seqinr" href="/link/read.fasta?package=metacoder&version=0.2.0&to=seqinr" data-mini-rdoc="seqinr::read.fasta">read.fasta</a></code>.</dd>
 Either "input" or "file" must be supplied but not both.
</dl>

input

The path to a FASTA file containing sequences to use. Either
"input" or "file" must be supplied but not both.

file

Read sequences in an unknown format. This is meant to parse the sequence
input arguments of functions like <code><a rd-options="" href="/link/primersearch?package=metacoder&version=0.2.0" data-mini-rdoc="metacoder::primersearch">primersearch</a></code>.

internal

A set of tools for parsing, manipulating, and graphing data
classified by a hierarchy (e.g. a taxonomy).

Zachary Foster

metacoder

Tools for Parsing, Manipulating, and Graphing Taxonomic
Abundance Data

Niklaus Grunwald

parse_seq_input function

(<code>character</code>) One of the following:<dl class='dl-horizontal'>
 <dt>A character vector of sequences</dt><dd>See the example below for what this
 looks like. The parser <code><a rd-options='' href='read_fasta'>read_fasta</a></code> produces output like this.</dd>
 <dt>A list of character vectors</dt><dd>Each vector should have one base per element.</dd>
 <dt>A "DNAbin" object</dt><dd>This is the result of parsers like
 <code><a rd-options='ape' href='read.FASTA'>read.FASTA</a></code>.</dd>
 <dt>A list of "SeqFastadna" objects</dt><dd>This is the result of parsers like
 <code><a rd-options='seqinr' href='read.fasta'>read.fasta</a></code>.</dd>
 Either "input" or "file" must be supplied but not both.
</dl>

Read sequences in an unknown format. This is meant to parse the sequence
input arguments of functions like <code><a rd-options='' href='primersearch'>primersearch</a></code>.

parse_seq_input: Read sequences in an unknown format

Description

Usage

Arguments

Value