/usr/bin/bp_oligo_count 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 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 | #!/usr/bin/perl
#
# oligomer_freq.pl
# We use this to determine what primers are useful for frequent priming of
# nucleic acid for random labeling
# Input: Sequence file, oligomer length
# Output: Tab-delimited text file of oligomer frequencies
# Written July 2, 2001
# Charles C. Kim
###########
# MODULES #
###########
use Bio::Seq;
use Bio::SeqIO;
use Getopt::Long;
#########################
# VARIABLES & FILENAMES #
#########################
use strict;
use warnings;
my ($format, $infile, $help, $outfile, $oligomerlength) = ('fasta');
GetOptions(
'f|format:s' => \$format,
'i|in|s|sequence:s' => \$infile,
'h|help|?' => \$help,
'o|out:s' => \$outfile,
'length:i' => \$oligomerlength
);
my $USAGE = "Usage:\toligo_count [-h/--help] [-l/--length OLIGOLENGTH]\n".
"\t[-f/--format SEQFORMAT] [-i/--in/-s/--sequence SEQFILE]\n".
"\t[-o/--out OUTFILE]\n".
"\tDefault SEQFORMAT is fasta\n";
print $USAGE and exit if $help;
unless ($infile ) {
print 'Enter your concatenated FASTA sequence filename: ';
chomp ($infile=<STDIN>);
}
unless (-e $infile) { die "$infile not found\n"; }
if ($outfile) {
if (-e $outfile) {
print "$outfile already exists! Overwrite (Y/N)? ";
chomp ($_ = <STDIN>);
while (/[^yn]/i) {
print 'Y or N, please: ';
chomp ($_ = <STDIN>);
}
if (/n/i) { die "$outfile not overwritten.\n"; }
}
#} else {
# print 'Enter an output filename: ';
# chomp ($outfile=<STDIN>);
# if (-e $outfile) {
# print "$outfile already exists! Overwrite (Y/N)? ";
# chomp ($_ = <STDIN>);
# while (/[^yn]/i) {
# print 'Y or N, please: ';
# chomp ($_ = <STDIN>);
# }
# if (/n/i) { die "$outfile not overwritten.\n"; }
# }
}
unless ($oligomerlength) {
while () {
print 'Enter an oligomer length to count: ';
chomp($oligomerlength=<STDIN>);
if ($oligomerlength !~ /\d/) {
print "Value is non-numeric!\n";
}
else {last;}
}
}
########
# MAIN #
########
if ($oligomerlength >= 9) {
print "An oligomer length of $oligomerlength will generate ";
print 4 ** $oligomerlength, " combinations,\nwhich could cause ";
print "an out of memory error. Proceed? (y/n) ";
chomp($_=<STDIN>);
if (/y/i) { ; }
else { die "Program terminated\n"; }
}
my @oligoseqs = &generate_all_oligos($oligomerlength);
my %oligos = ();
foreach (@oligoseqs) {
$oligos{$_} = 0;
}
my $in = Bio::SeqIO->new( -file => $infile,
-format => $format);
my $seqnumber = 0;
my $oligocounts = 0;
my $exception;
while (my $seq = $in->next_seq() ) {
my $len = $seq->length();
my $position = 1;
if ($position+$oligomerlength > $len) {
$exception = 2;
next;
}
$seq = uc $seq->seq; #string
$exception = 1 if $seq =~ /[^GATC]/;
while ($position + $oligomerlength-1 <= $len) {
$oligos{substr $seq, $position-1, $oligomerlength}++;
$position++;
if ($position%250000 == 0) {print "$position\n";}
}
$oligocounts += $position-1;
$seqnumber++;
}
my $OUTFILE;
if ($outfile) {
open $OUTFILE, '>', $outfile or die "Could not open file '$outfile': $!\n";
} else {
open $OUTFILE, '>-'; # STDOUT
}
print $OUTFILE "$seqnumber sequences analyzed\n";
print $OUTFILE "$oligocounts total $oligomerlength-mers counted\n";
print $OUTFILE "$oligomerlength-mer\tNumber\tFrequency\n";
foreach my $key (sort keys %oligos) {
print $OUTFILE "$key\t$oligos{$key}\t", $oligos{$key}/$oligocounts, "\n";
}
close $OUTFILE;
if ($exception) {
if ($exception == 1) {
print "Non-standard (non-GATC) bases were found in sequence\n";
}
if ($exception == 2) {
print "Oligomer length greater than sequence length\n";
}
}
#¬ify();
###############
# SUBROUTINES #
###############
sub generate_all_oligos {
my $oligolength = $_[0];
my $iter = 1;
my @newarray = qw{A C G T};
my @bases = qw{A C G T};
while ($iter < $oligolength) {
my @oldarray = @newarray;
@newarray = ();
foreach my $oligoseq (@oldarray) {
foreach my $newbase (@bases) {
push @newarray, $oligoseq . $newbase;
}
}
$iter++;
}
return @newarray;
}
# if you wanted to be notified about status of running
#my $EMAILADDRESS = undef;
#die("Must change script to a valid email addres for notification")
# unless( defined $EMAILADDRESS );
#sub notify {
# $address = $EMAILADDRESS;
# $address = $_[0] if $_[0];
# open(SENDMAIL, "|/usr/lib/sendmail -oi -t") or die "Can't fork for sendmail: $!\n";
# print SENDMAIL <<"EOF";
#From: Computer
#To: $address
#Subject: Program Finished
#
#EOF
# close(SENDMAIL) or warn "sendmail didn't close nicely";
#}
__END__
=head1 NAME
bp_oligo_count - oligo count and frequency
=head1 SYNOPSIS
Usage: bp_oligo_count [-h/--help] [-l/--length OLIGOLENGTH]
[-f/--format SEQFORMAT] [-i/--in/-s/--sequence SEQFILE]
[-o/--out OUTFILE]
=head1 DESCRIPTION
This scripts counts occurrence and frequency for all oligonucleotides
of given length.
It can be used to determine what primers are useful for
frequent priming of nucleic acid for random labeling.
Note that this script could be run by utilizing the compseq
program which is part of EMBOSS.
=head1 OPTIONS
The default sequence format is fasta. If no outfile is given, the
results will be printed to standard out. All other options can entered
interactively.
=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 - Charles C. Kim
Email cckim@stanford.edu
=head1 HISTORY
Written July 2, 2001
Submitted to bioperl scripts project 2001/08/06
E<gt>E<gt> 100 x speed optimization by Heikki Lehvaslaiho
=cut
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