fa_rename

Tools for reading and writing biological sequences in multiple
formats, including 'FASTA', 'PHYLIP', 'CLUSTAL', 'STOCKHOLM', 'MEGA' and
'GenBank'. Supports interleaved and sequential layouts where applicable,
and reads or writes gzip, bzip2 and xz compressed files transparently.
Converts between formats, renames sequences via a two-column mapping,
summarizes sequence counts, lengths, GC content and ambiguous characters,
and manipulates sequence sets (e.g., filtering by patterns and computing
consensus sequences from alignments). Also includes functions to download
nucleotide records from NCBI by accession.

Guangchuang Yu

seqmagick

Sequence Manipulation Utilities

fa_rename function

<dl><dt>fasfile</dt>
<dd>fasta file</dd>
<dt>mapping_file</dt>
<dd>mapping file</dd>
<dt>position</dt>
<dd>rename token at specific position</dd>
<dt>sep</dt>
<dd>sepator to divide token</dd>
<dt>mode</dt>
<dd>one of 'replace', 'prefix' or 'suffix'</dd>
<dt>outfile</dt>
<dd>output file</dd></dl>

Arguments

Author

fa_rename — fa_rename

<dl>

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


<dt>mapping_file</dt>
<dd>mapping file</dd>


<dt>position</dt>
<dd>rename token at specific position</dd>


<dt>sep</dt>
<dd>sepator to divide token</dd>


<dt>mode</dt>
<dd>one of 'replace', 'prefix' or 'suffix'</dd>


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

</dl>

fa_rename: fa_rename

Description

Usage

Value

Arguments

Author