scripts/seq/bp_seqconvert.pl

   1 #!perl
   2
   3 use strict;
   4 use warnings;
   5 use Getopt::Long;
   6 use Bio::SeqIO;
   7
   8 my $help;
   9 my $from=undef;
  10 my $to=undef;
  11
  12 ### please add to this list (see the modules under Bio/SeqIO):
  13 my @known_formats=
  14   qw(gcg fasta ace raw fastq phd pir scf swiss genbank locuslink
  15      embl game qual bsml tab raw abi chado alf ctf exp ztr pln
  16      chaosxml chadoxml yaml tigr tigrxml agave chaos kegg interpro
  17      lasergene strider gbdriver embldriver swissdriver);
  18
  19 my $script=substr($0, 1+rindex($0,'/'));
  20 my $usage="Usage:
  21
  22   $script --from in-format --to out-format < file.in-format > file.out-format
  23
  24 Known formats:\n  " . join(' ', @known_formats) . "\n\n";
  25
  26 die $usage unless
  27   &GetOptions( 'from:s'   => \$from,
  28                'to:s'     => \$to,
  29                'h|help'   => \$help
  30              )
  31   && !$help &&  $from && $to
  32   && grep($from eq $_, @known_formats)
  33   && grep($to eq $_, @known_formats);
  34
  35 my $in  = Bio::SeqIO->newFh(-fh => \*STDIN , '-format' => $from);
  36 my $out = Bio::SeqIO->newFh(-fh=> \*STDOUT, '-format' => $to);
  37
  38 print $out $_ while <$in>;
  39
  40
  41 __END__
  42
  43 =head1 NAME
  44
  45 bp_seqconvert - generic BioPerl sequence format converter
  46
  47 =head1 SYNOPSIS
  48
  49   bp_seqconvert --from in-format --to out-format < file.in-format > file.out-format
  50   # or
  51   bp_seqconvert -f in-format -t out-format < file.in-format > file.out-format
  52
  53 =head1 DESCRIPTION
  54
  55 This script gives command line interface to BioPerl Bio::SeqIO.
  56
  57 =head1 SEE ALSO
  58
  59 L<Bio::SeqIO>
  60 L<bp_sreformat.PLS> for similar functionality which also supports AlignIO.
  61
  62 =head1 FEEDBACK
  63
  64 =head2 Mailing Lists
  65
  66 User feedback is an integral part of the evolution of this and other
  67 Bioperl modules. Send your comments and suggestions preferably to
  68 the Bioperl mailing list.  Your participation is much appreciated.
  69
  70   bioperl-l@bioperl.org                  - General discussion
  71   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  72
  73 =head2 Reporting Bugs
  74
  75 Report bugs to the Bioperl bug tracking system to help us keep track
  76 of the bugs and their resolution. Bug reports can be submitted via the
  77 web:
  78
  79   https://github.com/bioperl/bioperl-live/issues
  80
  81 =head1 AUTHOR - Philip Lijnzaad
  82
  83 Email E<lt>p.lijnzaad-at-med.uu.nlE<gt>
  84
  85 =cut
  86
  87 __END__