added mutate_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@527 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/mutate_seq b/bp_bin/mutate_seq
new file mode 100755 (executable)
index 0000000..5d6d6db
--- /dev/null
+++ b/bp_bin/mutate_seq
@@ -0,0 +1,93 @@
+#!/usr/bin/env perl -w
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Introduce mutations into sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use strict;
+use Maasha::Common;
+use Maasha::Biopieces;
+use Maasha::Seq;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $type, $alph, $mutations, $seq_len, $record );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'number',  short => 'n', type => 'uint',   mandatory => 'no', default => undef, allowed => undef,             disallowed => 0     },
+        { long => 'percent', short => 'p', type => 'float',  mandatory => 'no', default => undef, allowed => undef,             disallowed => 0     },
+        { long => 'type',    short => 't', type => 'string', mandatory => 'no', default => undef, allowed => 'rna,dna,protein', disallowed => undef },
+    ]   
+);
+
+Maasha::Common::error( qq(both --number and --percent specified) ) if     $options->{ "number" } and     $options->{ "percent" };
+Maasha::Common::error( qq(no --number or --percent specified) )    if not $options->{ "number" } and not $options->{ "percent" };
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $record->{ "SEQ" } )
+    {
+        $seq_len   = length $record->{ "SEQ" };
+        $type      = $options->{ "type" } || Maasha::Seq::seq_guess_type( $record->{ "SEQ" } );
+        $alph      = Maasha::Seq::seq_alph( $type );
+        $mutations = $options->{ "number" } || int( $seq_len * ( $options->{ "percent" } / 100 ) );
+
+        Maasha::Common::error( qq(mutations > sequence length: $mutations > $seq_len)  ) if $mutations > $seq_len;
+
+        $record->{ "SEQ" } = Maasha::Seq::seq_mutate( $record->{ "SEQ" }, $mutations, $alph );
+    }
+
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__

diff --git a/code_perl/Maasha/Seq.pm b/code_perl/Maasha/Seq.pm
index 42df6d3427c87b0833819e802c17ae5ec829d518..12839653b5fbb4dec3b992401c22eda77edce6b9 100644 (file)
--- a/code_perl/Maasha/Seq.pm
+++ b/code_perl/Maasha/Seq.pm
@@ -29,6 +29,8 @@ package Maasha::Seq;
 
 
 use strict;
+use POSIX qw( islower );
+use Maasha::Common;
 use Data::Dumper;
 use IPC::Open2;
 use List::Util qw( shuffle );
@@ -763,7 +765,7 @@ sub seq_generate
          $alph,   # sequence alphabet
        ) = @_;
 
-    # returns string
+    # Returns a string
 
     my ( $alph_len, $i, $seq );
     
@@ -777,6 +779,67 @@ sub seq_generate
 }
 
 
+sub seq_mutate
+{
+    # Martin A. Hansen, June 2009.
+
+    # Introduces a given number of random mutations in a 
+    # given sequence of a specified alphabet.
+
+    my ( $seq,         # sequence to mutate
+         $mutations,   # number of mutations
+         $alph,        # alphabet of sequence
+       ) = @_;
+
+    # Returns a string.
+
+    my ( $i, $pos, %lookup_hash );
+
+    $i = 0;
+
+    while ( $i < $mutations )
+    {
+        $pos = int( rand( length $seq ) );
+
+        if ( not exists $lookup_hash{ $pos } )
+        {
+            substr $seq, $pos, 1, res_mutate( substr( $seq , $pos, 1 ), $alph );
+
+            $lookup_hash{ $pos } = 1;
+        
+            $i++;
+        }
+    }
+
+    return $seq;
+}
+
+
+sub res_mutate
+{
+    # Martin A. Hansen, June 2009.
+
+    # Mutates a given residue to another from a given alphabet.
+
+    my ( $res,    # residue to mutate
+         $alph,   # alphabet
+       ) = @_;
+
+    # Returns a char.
+
+    my ( $alph_len, $new );
+
+    $alph_len = scalar @{ $alph };
+    $new      = $res;
+
+    while ( uc $new eq uc $res ) {
+        $new = $alph->[ int( rand( $alph_len ) ) ];
+    }
+
+    return POSIX::islower( $res ) ? lc $new : uc $new;
+}
+
+
 sub seq_shuffle
 {
     # Martin A. Hansen, December 2007.
@@ -786,7 +849,7 @@ sub seq_shuffle
     my ( $seq,   # sequence string
        ) = @_;
 
-    # Returns string.
+    # Returns a string.
 
     my ( @list );