bin/bp_translate_seq

   1 #!/usr/bin/perl
   2 use strict;
   3 use warnings;
   4
   5 =head1 NAME
   6
   7 bp_translate_seq - translates a sequence
   8
   9 =head1 SYNOPSIS
  10
  11 bp_translate_seq E<lt> cdna_cds.fa E<gt> protein.fa
  12
  13 =head1 DESCRIPTION
  14
  15 The script will translate one fasta file (on stdin) to protein on stdout
  16
  17 =head1 FEEDBACK
  18
  19 =head2 Mailing Lists
  20
  21 User feedback is an integral part of the evolution of this and other
  22 Bioperl modules. Send your comments and suggestions preferably to
  23 the Bioperl mailing list.  Your participation is much appreciated.
  24
  25   bioperl-l@bioperl.org                  - General discussion
  26   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  27
  28 =head2 Reporting Bugs
  29
  30 Report bugs to the Bioperl bug tracking system to help us keep track
  31 of the bugs and their resolution. Bug reports can be submitted via
  32 email or the web:
  33
  34   https://github.com/bioperl/bioperl-live/issues
  35
  36 =head1 AUTHOR
  37
  38   Ewan Birney E<lt>birney@ebi.ac.ukE<gt>
  39
  40 =cut
  41
  42 use Bio::SeqIO;
  43 use Getopt::Long;
  44
  45 my ($format,$outfile) = 'fasta';
  46
  47 GetOptions(
  48     'f|format:s'  => \$format,
  49     'o|out|outfile:s' => \$outfile,
  50     );
  51
  52 my $oformat = 'fasta';
  53
  54 # this implicity uses the <> file stream
  55 my $seqin = Bio::SeqIO->new( -format => $format, -fh => \*ARGV);
  56 my $seqout;
  57 if( $outfile ) {
  58     $seqout = Bio::SeqIO->new( -format => $oformat, -file => ">$outfile" );
  59 } else {
  60 # defaults to writing to STDOUT
  61     $seqout = Bio::SeqIO->new( -format => $oformat );
  62 }
  63 while( (my $seq = $seqin->next_seq()) ) {
  64         my $pseq = $seq->translate();
  65         $seqout->write_seq($pseq);
  66 }
  67
  68 __END__