#!/home/passala/miniconda3/envs/Genomealign/bin/perl

use strict;
use warnings;
use Getopt::Long;
use Bio::SeqIO;

my $help;
my $from=undef;
my $to=undef;

### please add to this list (see the modules under Bio/SeqIO):
my @known_formats=
  qw(gcg fasta ace raw fastq phd pir scf swiss genbank locuslink
     embl game qual bsml tab raw abi chado alf ctf exp ztr pln
     chaosxml chadoxml yaml tigr tigrxml agave chaos kegg interpro
     lasergene strider gbdriver embldriver swissdriver);

my $script=substr($0, 1+rindex($0,'/'));
my $usage="Usage:

  $script --from in-format --to out-format < file.in-format > file.out-format

Known formats:\n  " . join(' ', @known_formats) . "\n\n";

die $usage unless
  &GetOptions( 'from:s'   => \$from,
               'to:s'     => \$to,
               'h|help'   => \$help
	     )
  && !$help &&  $from && $to
  && grep($from eq $_, @known_formats)
  && grep($to eq $_, @known_formats);

my $in  = Bio::SeqIO->newFh(-fh => \*STDIN , '-format' => $from);
my $out = Bio::SeqIO->newFh(-fh=> \*STDOUT, '-format' => $to);

print $out $_ while <$in>;


__END__

=head1 NAME

bp_seqconvert - generic BioPerl sequence format converter

=head1 SYNOPSIS

  bp_seqconvert --from in-format --to out-format < file.in-format > file.out-format
  # or
  bp_seqconvert -f in-format -t out-format < file.in-format > file.out-format

=head1 DESCRIPTION

This script gives command line interface to BioPerl Bio::SeqIO. 

=head1 SEE ALSO

L<Bio::SeqIO>
L<bp_sreformat.PLS> for similar functionality which also supports AlignIO.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Philip Lijnzaad

Email E<lt>p.lijnzaad-at-med.uu.nlE<gt>

=cut

__END__