/usr/bin/bp_gccalc is in bioperl 1.7.1-2.
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 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 | #!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
use Bio::Tools::SeqStats;
use Getopt::Long;
my $format = 'fasta';
my $file;
my $help =0;
my $aggregate;
GetOptions(
'f|format:s' => \$format,
'i|in:s' => \$file,
'h|help|?' => \$help,
'a|aggregate!'=> \$aggregate,
);
my $USAGE = "usage: gccalc.pl -f format -i filename\n";
if( $help ) {
die $USAGE;
}
$file = shift unless $file;
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 => $format,
-fh => \*STDIN);
}
my ($total_base, $total_gc);
while( my $seq = $seqin->next_seq ) {
next if( $seq->length == 0 );
if( $seq->alphabet eq 'protein' ) {
warn("gccalc does not work on amino acid sequences ...skipping this seq");
next;
}
my $seq_stats = Bio::Tools::SeqStats->new('-seq'=>$seq);
my $hash_ref = $seq_stats->count_monomers(); # for DNA sequence
print "Seq: ", $seq->display_id, " ";
print $seq->desc if $seq->desc;
print " Len:", $seq->length, "\n";
$total_base += $seq->length;
$total_gc += $hash_ref->{'G'} + $hash_ref->{'C'};
printf "GC content is %.4f\n", ($hash_ref->{'G'} + $hash_ref->{'C'}) /
$seq->length();
foreach my $base (sort keys %{$hash_ref}) {
print "Number of bases of type ", $base, "= ", $hash_ref->{$base},"\n";
}
print "--\n";
}
if( $aggregate ) {
printf "Total GC content is %.4f out of %d bases\n", $total_gc / $total_base, $total_base;
}
# alternatively one could use code submitted by
# cckim@stanford.edu
sub calcgc {
my $seq = $_[0];
my @seqarray = split('',$seq);
my $count = 0;
foreach my $base (@seqarray) {
$count++ if $base =~ /[G|C]/i;
}
my $len = $#seqarray+1;
return $count / $len;
}
__END__
=head1 NAME
bp_gccalc - GC content of nucleotide sequences
=head1 SYNOPSIS
bp_gccalc [-f/--format FORMAT] [-h/--help] filename
or
bp_gccalc [-f/--format FORMAT] < filename
or
bp_gccalc [-f/--format FORMAT] -i filename
=head1 DESCRIPTION
This scripts prints out the GC content for every nucleotide sequence
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_gccalc filename
=item named argument
bp_gccalc -i filename
=item standard input
bp_gccalc < 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 script code (see bottom) submitted by cckim@stanford.edu
Submitted as part of bioperl script project 2001/08/06
=cut
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