scripts/seq/bp_make_mrna_protein.pl

   1 #!perl
   2 #
   3 =head1 NAME
   4
   5 bp_make_mrna_protein - Convert an input mRNA/cDNA sequence into protein
   6
   7 =head1 DESCRIPTION
   8
   9 Convert an input mRNA/cDNA sequence into protein using translate()
  10
  11   -f/--frame           Specifies frame [0,1,2]
  12
  13 One can also specify:
  14
  15   -t/--terminator      Stop Codon character (defaults to '*')
  16   -u/--unknown         Unknown Protein character (defaults to 'X')
  17   -cds/--fullcds       Expected Full CDS (with start and Stop codon)
  18   -throwOnError        Throw error if no Full CDS (defaults to 0)
  19   -if/--format         Input format (defaults to FASTA/Pearson)
  20   -of/--format         Output format (defaults to FASTA/Pearson)
  21   -o/--output          Output Filename (defaults to STDOUT)
  22   -i/--input           Input Filename (defaults to STDIN)
  23   -ct/--codontable     Codon table to use (defaults to '1')
  24
  25 See L<Bio::PrimarySeq> for more information on codon tables
  26 and the translate() method
  27
  28 =head1 AUTHOR - Jason Stajich
  29
  30   Email jason-at-bioperl-dot-org
  31
  32 =cut
  33
  34 use strict;
  35 use warnings;
  36 use Bio::SeqIO;
  37 use Getopt::Long;
  38
  39 use vars qw($USAGE);
  40
  41 BEGIN {
  42     $USAGE =
  43 qq{make_mrna_protein.pl < file.fa > file.prots
  44 -f/--frame            Translation Frame (0,1,2) are valid (defaults to '0')
  45 -t/--terminator     Stop Codon Character ('*' by default)
  46 -u/--unknown          Unknown Protein character (defaults to 'X')
  47 -ct/--codontable      Codon table to use (defaults to '1')
  48                       (see Bio::PrimarySeq for more information)
  49 -cds/--fullcds        Expected Full CDS (with start and Stop codon)
  50 -throwOnError         Throw an error if no Full CDS (defaults to 0)
  51 -if/--iformat         Input format (defaults to FASTA/Pearson)
  52 -of/--oformat         Output format (defaults to FASTA/Pearson)
  53 -o/--output           Output Filename (defaults to STDOUT)
  54 -i/--input            Input Filename (defaults to STDIN)
  55 };
  56
  57 }
  58 my ($iformat, $oformat, $frame, $termchar, $unknownProt, $codontable, $fullCDS,
  59     $throw_on_Incomp_CDS, $help) = ('fasta','fasta', 0, undef, undef, 1, 0, 0);
  60 my ($input,$output);
  61
  62 GetOptions('f|frame:s'       => \$frame,
  63                           't|terminator:s'  => \$termchar,
  64                           'u|unknown:s'     => \$unknownProt,
  65                           'ct|codontable:s' => \$codontable,
  66                           'cds|fullcds'     => \$fullCDS,
  67                           'throwOnError'    => \$throw_on_Incomp_CDS,
  68                           'h|help'          => \$help,
  69                           'i|input:s'       => \$input,
  70                           'if|iformat:s'    => \$iformat,
  71                           'of|oformat:s'    => \$oformat,
  72                           'o|output:s'      => \$output,
  73                          );
  74
  75 die $USAGE if( $help );
  76
  77 my ($in,$out);
  78 if( $input ) {
  79         $in = new Bio::SeqIO('-format' => $iformat, '-file' => $input);
  80 } else {
  81         $in = new Bio::SeqIO('-format' => $iformat, '-fh' => \*STDIN);
  82 }
  83
  84 if( $output ) {
  85         $out = new Bio::SeqIO('-format' => $oformat, '-file' => ">$output" );
  86 } else {
  87         $out = new Bio::SeqIO('-format' => $oformat );
  88 }
  89
  90 while( my $seq = $in->next_seq ) {
  91     my $protseq = $seq->translate(-terminator => $termchar,
  92                                                                                          -unknown => $unknownProt,
  93                                                                                          -frame => $frame,
  94                                                                                          -codontable_id => $codontable,
  95                                                                                          -complete => $fullCDS,
  96                                                                                          -throw => $throw_on_Incomp_CDS );
  97     $out->write_seq($protseq);
  98 }
  99
 100 __END__