replaceInside

replace character for example from '-' to 'N' of fasta sequence that only applied inside sequence
any '-' character at start/end of the sequence (aligned seqs may contains '-' at prefix/suffix) will not be replaced

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

replaceInside function

<dl><dt>fasfile</dt>
<dd>fasta file</dd>
<dt>from</dt>
<dd>character to be replaced, '-' by default</dd>
<dt>to</dt>
<dd>replace 'from' to 'to', 'N' by default</dd>
<dt>outfile</dt>
<dd>output file</dd></dl>

Arguments

Author

replaceInside — replaceInside

<dl>

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


<dt>from</dt>
<dd>character to be replaced, '-' by default</dd>


<dt>to</dt>
<dd>replace 'from' to 'to', 'N' by default</dd>


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

</dl>

replaceInside: replaceInside

Description

Usage

Value

Arguments

Author