/usr/bin/bp_translate_seq is in bioperl 1.6.901-2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 | #!/usr/bin/perl -w
eval 'exec /usr/bin/perl -w -S $0 ${1+"$@"}'
if 0; # not running under some shell
use strict;
=head1 NAME
translate_seq - translates a sequence
=head1 SYNOPSIS
translate_seq E<lt> cdna_cds.fa E<gt> protein.fa
=head1 DESCRIPTION
The script will translate one fasta file (on stdin) to protein on stdout
=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
email or the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Ewan Birney E<lt>birney@ebi.ac.ukE<gt>
=cut
use Bio::SeqIO;
use Getopt::Long;
my ($format) = 'fasta';
GetOptions(
'format:s' => \$format,
);
my $oformat = 'fasta';
# this implicity uses the <> file stream
my $seqin = Bio::SeqIO->new( -format => $format, -file => shift);
my $seqout = Bio::SeqIO->new( -format => $oformat, -file => ">-" );
while( (my $seq = $seqin->next_seq()) ) {
my $pseq = $seq->translate();
$seqout->write_seq($pseq);
}
__END__
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