--- /dev/null
+#!/usr/bin/env perl
+
+# Copyright (C) 2007-2010 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Trim sequence ends for residues with a low quality score.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+use Maasha::Fastq;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $left, $right, $pos_l, $pos_r );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'min', short => 'm', type => 'uint', mandatory => 'no', default => 15, allowed => undef, disallowed => 0 },
+ { long => 'trim', short => 't', type => 'string', mandatory => 'no', default => 'both', allowed => 'left,right,both', disallowed => undef },
+ ]
+);
+
+$right = 1 if $options->{ 'trim' } eq 'right';
+$left = 1 if $options->{ 'trim' } eq 'left';
+$right = 1 if $options->{ 'trim' } eq 'both';
+$left = 1 if $options->{ 'trim' } eq 'both';
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( exists $record->{ 'SEQ' } and exists $record->{ 'SCORES' } )
+ {
+ if ( $right )
+ {
+ $pos_r = Maasha::Fastq::trim_right( $record->{ 'SCORES' }, $options->{ 'min' } );
+
+ $record->{ 'SEQ' } = substr $record->{ 'SEQ' }, 0, $pos_r + 1;
+ $record->{ 'SCORES' } = substr $record->{ 'SCORES' }, 0, $pos_r + 1;
+ $record->{ 'TRIM_RIGHT' } = $pos_r;
+ }
+
+ if ( $left )
+ {
+ $pos_l = Maasha::Fastq::trim_left( $record->{ 'SCORES' }, $options->{ 'min' } );
+
+ $record->{ 'SEQ' } = substr $record->{ 'SEQ' }, $pos_l;
+ $record->{ 'SCORES' } = substr $record->{ 'SCORES' }, $pos_l;
+ $record->{ 'TRIM_LEFT' } = $pos_l;
+ }
+
+ $record->{ 'SEQ_LEN' } = length $record->{ 'SEQ' };
+ }
+
+ 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__
}
+int trim_left( char *scores, int min )
+{
+ /* Martin A. Hansen, June 2010 */
+
+ /* Starting from the left in a score string, */
+ /* locate the position when the score is above */
+ /* a given min.*/
+
+ int pos = 0;
+
+ while ( pos < strlen( scores ) && solexa2dec( scores[ pos ] ) <= min ) {
+ pos++;
+ }
+
+ return pos;
+}
+
+
+int trim_right( char *scores, int min )
+{
+ /* Martin A. Hansen, June 2010 */
+
+ /* Starting from the right in a score string, */
+ /* locate the position when the score is above */
+ /* a given min.*/
+
+ int len = strlen( scores );
+ int pos = len;
+
+ while ( pos > 0 && solexa2dec( scores[ pos ] ) <= min ) {
+ pos--;
+ }
+
+ if ( pos == 0 ) {
+ pos = len;
+ }
+
+ return pos;
+}
+
END_C
# Given the script name determine the path of the wiki file with the usage info.
def wiki_path
- path = ENV["BP_DIR"] + "/bp_usage/" + File.basename(@script_path, ".rb") + ".wiki"
+ path = ENV["BP_DIR"] + "/bp_usage/" + File.basename(@script_path) + ".wiki"
raise "No such wiki file: #{path}" unless File.file? path
path
end
def log(exit_status)
time1 = Time.new.strftime("%Y-%m-%d %X")
user = ENV["USER"]
- script = File.basename($0, ".rb")
+ script = File.basename($0)
stream = File.open(path)
time0, args, tmp_dir = stream.first.split(";")
# Path to status file
def path
user = ENV["USER"]
- script = File.basename($0, ".rb")
+ script = File.basename($0)
pid = $$
path = ENV["BP_TMP"] + "/" + [user, script, pid, "status"].join(".")
end