/usr/bin/bp_aacomp is in bioperl 1.6.924-3.
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 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 | #!/usr/bin/perl
eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
if 0; # not running under some shell
use strict;
use warnings;
use Carp;
use Bio::SeqIO;
use Getopt::Long;
use Bio::SeqUtils;
use Bio::Tools::IUPAC;
my $table = new Bio::SeqUtils;
my @BASES = $table->valid_aa(0);
my %all = $table->valid_aa(2);
my ($file,$format,$help) = ( undef, 'fasta');
GetOptions(
'i|in:s' => \$file,
'f|format:s' => \$format,
'h|help|?' => \$help,
);
my $USAGE = "usage: aacomp [-f format] filename\n\tdefault format is fasta\n";
$file = shift unless $file;
die $USAGE if $help;
my $seqin;
if( defined $file ) {
print "Could not open file [$file]\n$USAGE" and exit unless -e $file;
$seqin = new Bio::SeqIO(-format => $format,
-file => $file);
} else {
$seqin = new Bio::SeqIO(-format => $format,
-fh => \*STDIN);
}
my %composition;
my $total;
foreach my $base ( @BASES ) {
$composition{$base} = 0;
}
while ( my $seq = $seqin->next_seq ) {
if( $seq->alphabet ne 'protein' ) {
confess("Must only provide amino acid sequences to aacomp...skipping this seq");
next;
}
foreach my $base ( split(//,$seq->seq()) ) {
$composition{uc $base}++;
$total++;
}
}
printf("%d aa\n",$total);
printf("%5s %4s\n", 'aa', '#' );
my $ct = 0;
foreach my $base ( @BASES ) {
printf(" %s %s %3d\n", $base, $all{$base}, $composition{$base} );
$ct += $composition{$base};
}
printf( "%6s %s\n", '','-'x5);
printf( "%6s %3d\n", '',$ct);
__END__
=head1 NAME
bp_aacomp - amino acid composition of protein sequences
=head1 SYNOPSIS
bp_aacomp [-f/--format FORMAT] [-h/--help] filename
or
bp_aacomp [-f/--format FORMAT] < filename
or
bp_aacomp [-f/--format FORMAT] -i filename
=head1 DESCRIPTION
This scripts prints out the count of amino acids over all protein
sequences from the input file.
=head1 OPTIONS
The default sequence format is fasta.
The sequence input can be provided using any of the three methods:
=over 3
=item unnamed argument
bp_aacomp filename
=item named argument
bp_aacomp -i filename
=item standard input
bp_aacomp < filename
=back
=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
Email jason@bioperl.org
=head1 HISTORY
Based on aacomp.c from an old version of EMBOSS
=cut
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