/usr/bin/bp_seq_length is in bioperl 1.7.2-2.
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 66 67 | #!/usr/bin/perl
=head1 NAME
bp_seq_length.pl - lists the number of bases and number of sequences in specified sequence database files
=head1 SYNOPSIS
bp_seq_length.pl *.fa
=head1 DESCRIPTION
bp_seq_length.pl will report the total number of residues and total number of individual sequences contained within a specified sequence database file.
=head1 OPTIONS
-f/--format - Specify the database format ('fasta' is default).
This script uses SeqIO and as such formats are
limited to those which SeqIO system supports.
=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 - Jason Stajich
Jason Stajich E<lt>jason@bioperl.orgE<gt>
=cut
use strict;
use warnings;
use Bio::SeqIO;
use Getopt::Long;
my $format = 'fasta';
GetOptions('f|format:s' => \$format);
exec('perldoc',$0) unless @ARGV;
foreach my $f ( @ARGV ) {
my $in = new Bio::SeqIO(-file => $f,
-format => $format);
my $len = 0;
my $count = 0;
while( my $seq = $in->next_seq ) {
$len += $seq->length();
$count++;
}
printf "%-10s %d bp $count sequences\n",$f,$len;
}
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