fa_filter

Supports reading and writing sequences for different formats (currently interleaved and sequential formats for 'FASTA' and 'PHYLIP'), file conversion, and manipulation (e.g. filter sequences that contain specify pattern, export consensus sequence from an alignment).

Guangchuang Yu

seqmagick

Sequence Manipulation Utilities

fa_filter function

<dl><dt>fasfile</dt>
<dd>input fasta file</dd>
<dt>pattern</dt>
<dd>keyword for filter</dd>
<dt>by</dt>
<dd>one of 'description' and 'sequence'</dd>
<dt>ignore.case</dt>
<dd>logical</dd>
<dt>outfile</dt>
<dd>output file</dd>
<dt>type</dt>
<dd>one of 'interleaved' and 'sequential'</dd></dl>

Arguments

Author

fa_filter — fa_filter

<dl>

<dt>fasfile</dt>
<dd>input fasta file</dd>


<dt>pattern</dt>
<dd>keyword for filter</dd>


<dt>by</dt>
<dd>one of 'description' and 'sequence'</dd>


<dt>ignore.case</dt>
<dd>logical</dd>


<dt>outfile</dt>
<dd>output file</dd>


<dt>type</dt>
<dd>one of 'interleaved' and 'sequential'</dd>

</dl>

fa_filter: fa_filter

Description

Usage

Value

Arguments

Author