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=item --mol-wt

Print lower and upper bound of molecular weight

=item --num-gaps-dna

Print number of non-ATCG's for a dna sequence. 

Redirect STDERR to a file to view non-ATCG positions, e.g.,:
 bioseq --num-gaps-dna seq.fas > out 2> log

=item --num-gaps-aa

Print number of non-AA's for a protein sequence. 

Redirect STDERR to a file to view non-AA positions, e.g.,:
 bioseq --num-gaps-aa seq.pep > out 2> log

=item --no-gaps, -g

Remove gaps

=item --num-seq, -n

Print number of sequences.

=item --output, -o 'format'

Output file format. By default, this is 'fasta'. For Genbank format, use 'genbank'. For EMBL format, use 'embl'.

=item --pick, -p 'tag:value'

Select a single sequence:

   --pick 'id:foo'        by id
   --pick 'order:2'       by order
   --pick 're:REGEX'      using a regular expression

Select a list of sequences:

   --pick 'id:foo,bar'    list by id
   --pick 'order:2,3'     list by order
   --pick 'order:2-10'    list by range
   --pick 'file:name'     id list in file, one id per line

=item --reloop, -R 'number'

Re-circularize a bacterial genome by starting at a specified position. For example, for sequence "ABCDE",  C<bioseq -R'2'> would generate "BCDEA".

=item --rename, -N 'file'; or --rename "id:old_name;new_name" (for replacing a single id)

Append sequence names specified by a file (two tab-separated columns: old_name, new_name), or a single id

=item --remove-stop, -X

Remove stop codons (e.g., for PAML input)

=item --restrict, -x 'RE'

Predicted fragments from digestion by a specified restriction enzyme. Disabled (not part of bioperl dist)

=item --restrict-coord 'RE'

Predicted fragments from digestion by a specified restriction enzyme.  Outputs cooridnates of overhangs in BED format. Disabled (not part of bioperl dist)

=item --revcom | -r

Reverse complement.

=item --sort 'id|length|file:<filename>'

Sort by id, length, or a file with an intended order of seq ids (Contributor: Jeffery Rosario; Fall 2017)

=item --split-cdhit 'cdhit .clstr file'

Parse cdhit output .clstr file and generate a FASTA file for each CDHIT family.

=item --subseq | -s 'beginning_index,ending_index'

Select substring (of the 1st sequence).

=item --syn-code 

Randomly substitute each codon with a synonymous one for a coding sequence

=item --translate | -t [1|3|6]

Translate in 1, 3, or 6 frames. e.g., -t1, -t3, or -t6.

=back

=head2 Common Options

=over 4

=item --help, -h

Print a brief help message and exit.

=item --man (but not "-m")

Print the manual page and exit.

=item --version, -V

Print current release version of this command and exit.

=back

=head1 SEE ALSO

=over 4

=item *

L<Bio::BPWrapper::SeqManipulations>, the underlying Perl Module

=item *

L<Qiu Lab wiki page|http://diverge.hunter.cuny.edu/labwiki/Bioutils>

=item *

L<Github project wiki page|https://github.com/bioperl/p5-bpwrapper/wiki>