=head1 NAME

recs-tofasta

=head1 USAGE

    Help from: --help-basic:
    Usage: recs-tofasta <options> [files]
       Outputs a FASTA-formatted sequence for each record.
    
       By default the keys "id", "description", and "sequence" are used to build the
       FASTA format. These defaults match up with what recs-fromfasta produces.
    
    Arguments:
       --id|-i <keyspec>            Record field to use for the sequence id
       --description|-d <keyspec>   Record field to use for the sequence description
       --sequence|-s <keyspec>      Record field to use for the sequence itself
       --width|w <#>                Format sequence blocks to # characters wide
       --oneline                    Format sequences on a single long line
       --filename-key|fk <keyspec>  Add a key with the source filename (if no
                                    filename is applicable will put NONE)
    
      Help Options:
          --help-all       Output all help for this script
          --help           This help screen
          --help-keys      Help on keygroups and keyspecs
          --help-keyspecs  Help on keyspecs, a way to index deeply and with regexes
    
    Examples:
      # Remove gaps from a fasta file
      recs-fromfasta seqs.fa | recs-xform '{{sequence}} =~ s/-//g' | recs-tofasta > seqs-nogaps.fa
    
    Help from: --help-keyspecs:
      KEY SPECS
       A key spec is short way of specifying a field with prefixes or regular
       expressions, it may also be nested into hashes and arrays. Use a '/' to nest
       into a hash and a '#NUM' to index into an array (i.e. #2)
    
       An example is in order, take a record like this:
    
         {"biz":["a","b","c"],"foo":{"bar 1":1},"zap":"blah1"}
         {"biz":["a","b","c"],"foo":{"bar 1":2},"zap":"blah2"}
         {"biz":["a","b","c"],"foo":{"bar 1":3},"zap":"blah3"}
    
       In this case a key spec of 'foo/bar 1' would have the values 1,2, and 3 in
       the respective records.
    
       Similarly, 'biz/#0' would have the value of 'a' for all 3 records
    
       You can also prefix key specs with '@' to engage the fuzzy matching logic
    
       Fuzzy matching works like this in order, first key to match wins
         1. Exact match ( eq )
         2. Prefix match ( m/^/ )
         3. Match anywehre in the key (m//)
    
       So, in the above example '@b/#2', the 'b' portion would expand to 'biz' and 2
       would be the index into the array, so all records would have the value of 'c'
    
       Simiarly, @f/b would have values 1, 2, and 3
    
       You can escape / with a \. For example, if you have a record:
       {"foo/bar":2}
    
       You can address that key with foo\/bar
    

=head1 SEE ALSO

L<App::RecordStream::Bio>

=cut

