-#!/usr/bin/env perl
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Locates and removes a specified adaptor sequence from sequences in stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Common;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $adaptor, $seq, $adaptor_len,
+ $seq_len, $offset, $max_match, $max_mismatch, $pos );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'adaptor', short => 'a', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { long => 'mismatches', short => 'm', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'offset', short => 'o', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 },
+ { long => 'remove', short => 'r', type => 'string', mandatory => 'no', default => 'after', allowed => 'before,after,skip', disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$max_mismatch = $options->{ "mismatches" };
+$offset = $options->{ "offset" };
+
+if ( not defined $offset ) {
+ $offset = 0;
+} else {
+ $offset--;
+}
+
+$adaptor = uc $options->{ "adaptor" };
+$adaptor_len = length $adaptor;
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $record->{ "SEQ" } )
+ {
+ $seq = uc $record->{ "SEQ" };
+ $seq_len = length $seq;
+
+ $pos = Maasha::Common::index_m( $seq, $adaptor, $seq_len, $adaptor_len, $offset, $max_mismatch );
+
+ $record->{ "ADAPTOR_POS" } = $pos;
+
+ if ( $pos >= 0 and $options->{ "remove" } ne "skip" )
+ {
+ if ( $options->{ "remove" } eq "after" )
+ {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, 0, $pos;
+ $record->{ "SEQ_LEN" } = $pos;
+ }
+ else
+ {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $pos + $adaptor_len;
+ $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
+ }
+ }
+
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+ else
+ {
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ $run_time_beg = Maasha::Biopieces::run_time();
+
+ Maasha::Biopieces::log_biopiece();
+}
+
+
+END
+{
+ Maasha::Biopieces::close_stream( $in );
+ Maasha::Biopieces::close_stream( $out );
+
+ $run_time_end = Maasha::Biopieces::run_time();
+
+ Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
-use Maasha::BioRun;
elsif ( $script eq "write_2bit" ) { script_write_2bit( $in, $out, $options ) }
elsif ( $script eq "write_solid" ) { script_write_solid( $in, $out, $options ) }
elsif ( $script eq "write_ucsc_config" ) { script_write_ucsc_config( $in, $out, $options ) }
- elsif ( $script eq "remove_adaptor" ) { script_remove_adaptor( $in, $out, $options ) }
elsif ( $script eq "remove_mysql_tables" ) { script_remove_mysql_tables( $in, $out, $options ) }
elsif ( $script eq "remove_ucsc_tracks" ) { script_remove_ucsc_tracks( $in, $out, $options ) }
elsif ( $script eq "plot_histogram" ) { script_plot_histogram( $in, $out, $options ) }
ylabel|Y=s
);
}
- elsif ( $script eq "remove_adaptor" )
- {
- @options = qw(
- adaptor|a=s
- mismatches|m=s
- remove|r=s
- offset|o=s
- );
- }
elsif ( $script eq "remove_mysql_tables" )
{
@options = qw(
{
Maasha::Common::error( qq(Argument to --$opt must be octal or decimal - not "$options{ $opt }") );
}
- elsif ( $opt eq "remove" and $script eq "remove_adaptor" and $options{ $opt } !~ /before|after|skip/ )
- {
- Maasha::Common::error( qq(Argument to --$opt must be before, after, or skip - not "$options{ $opt }") );
- }
}
Maasha::Common::error( qq(no --database specified) ) if $script eq "remove_ucsc_tracks" and not $options{ "database" };
}
-sub script_remove_adaptor
-{
- # Martin A. Hansen, August 2008.
-
- # Find and remove adaptor from sequences in the stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $adaptor, $seq, $adaptor_len, $seq_len, $offset, $max_match, $max_mismatch, $pos );
-
- $options->{ "remove" } ||= "after";
-
- $max_mismatch = $options->{ "mismatches" } || 0;
- $offset = $options->{ "offset" };
-
- if ( not defined $offset ) {
- $offset = 0;
- } else {
- $offset--;
- }
-
- $adaptor = uc $options->{ "adaptor" };
- $adaptor_len = length $adaptor;
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- if ( $record->{ "SEQ" } )
- {
- $seq = uc $record->{ "SEQ" };
- $seq_len = length $seq;
-
- $pos = Maasha::Common::index_m( $seq, $adaptor, $seq_len, $adaptor_len, $offset, $max_mismatch );
-
- $record->{ "ADAPTOR_POS" } = $pos;
-
- if ( $pos >= 0 and $options->{ "remove" } ne "skip" )
- {
- if ( $options->{ "remove" } eq "after" )
- {
- $record->{ "SEQ" } = substr $record->{ "SEQ" }, 0, $pos;
- $record->{ "SEQ_LEN" } = $pos;
- }
- else
- {
- $record->{ "SEQ" } = substr $record->{ "SEQ" }, $pos + $adaptor_len;
- $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
- }
- }
-
- Maasha::Biopieces::put_record( $record, $out );
- }
- else
- {
- Maasha::Biopieces::put_record( $record, $out );
- }
- }
-}
-
-
sub script_remove_mysql_tables
{
# Martin A. Hansen, November 2008.
projects / biopieces.git / commitdiff