From: martinahansen Date: Thu, 28 May 2009 11:46:06 +0000 (+0000) Subject: migrated remove_adaptor X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=736f89f17cce9d642088ec289d57f42ffe2668d1;p=biopieces.git migrated remove_adaptor git-svn-id: http://biopieces.googlecode.com/svn/trunk@445 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor index fdf5bd2..118bab3 100755 --- a/bp_bin/remove_adaptor +++ b/bp_bin/remove_adaptor @@ -1,6 +1,124 @@ -#!/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; diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm index 6a39e40..7d29d82 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -141,7 +141,6 @@ sub run_script 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 ) } @@ -400,15 +399,6 @@ sub get_options ylabel|Y=s ); } - elsif ( $script eq "remove_adaptor" ) - { - @options = qw( - adaptor|a=s - mismatches|m=s - remove|r=s - offset|o=s - ); - } elsif ( $script eq "remove_mysql_tables" ) { @options = qw( @@ -603,10 +593,6 @@ sub get_options { Maasha::Common::error( qq(Argument to --$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" }; @@ -2003,70 +1989,6 @@ sub script_plot_phastcons_profiles } -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.