-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Merge records in the stream based on identifier values to specific keys.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Common;
+use Maasha::Filesys;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $tmp_dir, $file1, $file2, $fh1, $fh2,
+ $key1, $key2, @keys1, @keys2, @vals1, @vals2, $num1, $num2, $num, $cmp, $i );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'keys', short => 'k', type => 'list', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { long => 'merge', short => 'm', type => 'string', mandatory => 'no', default => 'AandB', allowed => 'AandB,AorB,BorA,AnotB,BnotA', disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+
+$file1 = "$tmp_dir/merge_records1.tmp";
+$file2 = "$tmp_dir/merge_records2.tmp";
+
+$fh1 = Maasha::Filesys::file_write_open( $file1 );
+$fh2 = Maasha::Filesys::file_write_open( $file2 );
+
+$key1 = $options->{ "keys" }->[ 0 ];
+$key2 = $options->{ "keys" }->[ 1 ];
+
+$num = $key2 =~ s/n$//;
+$num1 = 0;
+$num2 = 0;
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( exists $record->{ $key1 } )
+ {
+ @keys1 = $key1;
+ @vals1 = $record->{ $key1 };
+
+ delete $record->{ $key1 };
+
+ map { push @keys1, $_; push @vals1, $record->{ $_ } } keys %{ $record };
+
+ print $fh1 join( "\t", @vals1 ), "\n";
+
+ $num1++;
+ }
+ elsif ( exists $record->{ $key2 } )
+ {
+ @keys2 = $key2;
+ @vals2 = $record->{ $key2 };
+
+ delete $record->{ $key2 };
+
+ map { push @keys2, $_; push @vals2, $record->{ $_ } } keys %{ $record };
+
+ print $fh2 join( "\t", @vals2 ), "\n";
+
+ $num2++;
+ }
+}
+
+close $fh1;
+close $fh2;
+
+if ( $num )
+{
+ Maasha::Common::run( "sort", "-k 1,1n $file1 > $file1.sort" ) and rename "$file1.sort", $file1;
+ Maasha::Common::run( "sort", "-k 1,1n $file2 > $file2.sort" ) and rename "$file2.sort", $file2;
+}
+else
+{
+ Maasha::Common::run( "sort", "-k 1,1 $file1 > $file1.sort" ) and rename "$file1.sort", $file1;
+ Maasha::Common::run( "sort", "-k 1,1 $file2 > $file2.sort" ) and rename "$file2.sort", $file2;
+}
+
+$fh1 = Maasha::Filesys::file_read_open( $file1 );
+$fh2 = Maasha::Filesys::file_read_open( $file2 );
+
+@vals1 = Maasha::Common::get_fields( $fh1 );
+@vals2 = Maasha::Common::get_fields( $fh2 );
+
+while ( $num1 > 0 and $num2 > 0 )
+{
+ undef $record;
+
+ if ( $num ) {
+ $cmp = $vals1[ 0 ] <=> $vals2[ 0 ];
+ } else {
+ $cmp = $vals1[ 0 ] cmp $vals2[ 0 ];
+ }
+
+ if ( $cmp < 0 )
+ {
+ if ( $options->{ 'merge' } =~ /^(AorB|AnotB)$/ )
+ {
+ for ( $i = 0; $i < @keys1; $i++ ) {
+ $record->{ $keys1[ $i ] } = $vals1[ $i ];
+ }
+
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+
+ @vals1 = Maasha::Common::get_fields( $fh1 );
+ $num1--;
+ }
+ elsif ( $cmp > 0 )
+ {
+ if ( $options->{ 'merge' } =~ /^(BorA|BnotA)$/ )
+ {
+ for ( $i = 0; $i < @keys2; $i++ ) {
+ $record->{ $keys2[ $i ] } = $vals2[ $i ];
+ }
+
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+
+ @vals2 = Maasha::Common::get_fields( $fh2 );
+ $num2--;
+ }
+ else
+ {
+ if ( $options->{ 'merge' } =~ /^(AandB|AorB|BorA)$/ )
+ {
+ for ( $i = 0; $i < @keys1; $i++ ) {
+ $record->{ $keys1[ $i ] } = $vals1[ $i ];
+ }
+
+ for ( $i = 1; $i < @keys2; $i++ ) {
+ $record->{ $keys2[ $i ] } = $vals2[ $i ];
+ }
+
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+
+ @vals1 = Maasha::Common::get_fields( $fh1 );
+ @vals2 = Maasha::Common::get_fields( $fh2 );
+ $num1--;
+ $num2--;
+ }
+}
+
+close $fh1;
+close $fh2;
+
+unlink $file1;
+unlink $file2;
+
+if ( $num1 > 0 and $options->{ 'merge' } =~ /^(AorB|AnotB)$/ )
+{
+ undef $record;
+
+ for ( $i = 0; $i < @keys1; $i++ ) {
+ $record->{ $keys1[ $i ] } = $vals1[ $i ];
+ }
+
+ Maasha::Biopieces::put_record( $record, $out );
+}
+
+if ( $num2 > 0 and $options->{ 'merge' } =~ /^(BorA|BnotA)$/ )
+{
+ undef $record;
+
+ for ( $i = 0; $i < @keys2; $i++ ) {
+ $record->{ $keys2[ $i ] } = $vals2[ $i ];
+ }
+
+ Maasha::Biopieces::put_record( $record, $out );
+}
+
+Maasha::Filesys::dir_remove( $tmp_dir );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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 "rename_keys" ) { script_rename_keys( $in, $out, $options ) }
elsif ( $script eq "uniq_vals" ) { script_uniq_vals( $in, $out, $options ) }
elsif ( $script eq "merge_vals" ) { script_merge_vals( $in, $out, $options ) }
- elsif ( $script eq "merge_records" ) { script_merge_records( $in, $out, $options ) }
elsif ( $script eq "sort_records" ) { script_sort_records( $in, $out, $options ) }
elsif ( $script eq "plot_histogram" ) { script_plot_histogram( $in, $out, $options ) }
elsif ( $script eq "plot_lendist" ) { script_plot_lendist( $in, $out, $options ) }
delimit|d=s
);
}
- elsif ( $script eq "merge_records" )
- {
- @options = qw(
- keys|k=s
- merge|m=s
- );
- }
elsif ( $script eq "sort_records" )
{
@options = qw(
}
-sub script_merge_records
-{
- # Martin A. Hansen, July 2008.
-
- # Merges records in the stream based on identical values of two given keys.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $merge, $record, $file1, $file2, $fh1, $fh2, $key1, $key2, @keys1, @keys2, @vals1, @vals2,
- $num1, $num2, $num, $cmp, $i );
-
- $merge = $options->{ "merge" } || "AandB";
-
- $file1 = "$BP_TMP/merge_records1.tmp";
- $file2 = "$BP_TMP/merge_records2.tmp";
-
- $fh1 = Maasha::Common::write_open( $file1 );
- $fh2 = Maasha::Common::write_open( $file2 );
-
- $key1 = $options->{ "keys" }->[ 0 ];
- $key2 = $options->{ "keys" }->[ 1 ];
-
- $num = $key2 =~ s/n$//;
- $num1 = 0;
- $num2 = 0;
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- if ( exists $record->{ $key1 } )
- {
- @keys1 = $key1;
- @vals1 = $record->{ $key1 };
-
- delete $record->{ $key1 };
-
- map { push @keys1, $_; push @vals1, $record->{ $_ } } keys %{ $record };
-
- print $fh1 join( "\t", @vals1 ), "\n";
-
- $num1++;
- }
- elsif ( exists $record->{ $key2 } )
- {
- @keys2 = $key2;
- @vals2 = $record->{ $key2 };
-
- delete $record->{ $key2 };
-
- map { push @keys2, $_; push @vals2, $record->{ $_ } } keys %{ $record };
-
- print $fh2 join( "\t", @vals2 ), "\n";
-
- $num2++;
- }
- }
-
- close $fh1;
- close $fh2;
-
- if ( $num )
- {
- Maasha::Common::run( "sort", "-k 1,1n $file1 > $file1.sort" ) and rename "$file1.sort", $file1;
- Maasha::Common::run( "sort", "-k 1,1n $file2 > $file2.sort" ) and rename "$file2.sort", $file2;
- }
- else
- {
- Maasha::Common::run( "sort", "-k 1,1 $file1 > $file1.sort" ) and rename "$file1.sort", $file1;
- Maasha::Common::run( "sort", "-k 1,1 $file2 > $file2.sort" ) and rename "$file2.sort", $file2;
- }
-
- $fh1 = Maasha::Common::read_open( $file1 );
- $fh2 = Maasha::Common::read_open( $file2 );
-
- @vals1 = Maasha::Common::get_fields( $fh1 );
- @vals2 = Maasha::Common::get_fields( $fh2 );
-
- while ( $num1 > 0 and $num2 > 0 )
- {
- undef $record;
-
- if ( $num ) {
- $cmp = $vals1[ 0 ] <=> $vals2[ 0 ];
- } else {
- $cmp = $vals1[ 0 ] cmp $vals2[ 0 ];
- }
-
- if ( $cmp < 0 )
- {
- if ( $merge =~ /^(AorB|AnotB)$/ )
- {
- for ( $i = 0; $i < @keys1; $i++ ) {
- $record->{ $keys1[ $i ] } = $vals1[ $i ];
- }
-
- Maasha::Biopieces::put_record( $record, $out );
- }
-
- @vals1 = Maasha::Common::get_fields( $fh1 );
- $num1--;
- }
- elsif ( $cmp > 0 )
- {
- if ( $merge =~ /^(BorA|BnotA)$/ )
- {
- for ( $i = 0; $i < @keys2; $i++ ) {
- $record->{ $keys2[ $i ] } = $vals2[ $i ];
- }
-
- Maasha::Biopieces::put_record( $record, $out );
- }
-
- @vals2 = Maasha::Common::get_fields( $fh2 );
- $num2--;
- }
- else
- {
- if ( $merge =~ /^(AandB|AorB|BorA)$/ )
- {
- for ( $i = 0; $i < @keys1; $i++ ) {
- $record->{ $keys1[ $i ] } = $vals1[ $i ];
- }
-
- for ( $i = 1; $i < @keys2; $i++ ) {
- $record->{ $keys2[ $i ] } = $vals2[ $i ];
- }
-
- Maasha::Biopieces::put_record( $record, $out );
- }
-
- @vals1 = Maasha::Common::get_fields( $fh1 );
- @vals2 = Maasha::Common::get_fields( $fh2 );
- $num1--;
- $num2--;
- }
- }
-
- close $fh1;
- close $fh2;
-
- unlink $file1;
- unlink $file2;
-
- if ( $num1 > 0 and $merge =~ /^(AorB|AnotB)$/ )
- {
- undef $record;
-
- for ( $i = 0; $i < @keys1; $i++ ) {
- $record->{ $keys1[ $i ] } = $vals1[ $i ];
- }
-
- Maasha::Biopieces::put_record( $record, $out );
- }
-
- if ( $num2 > 0 and $merge =~ /^(BorA|BnotA)$/ )
- {
- undef $record;
-
- for ( $i = 0; $i < @keys2; $i++ ) {
- $record->{ $keys2[ $i ] } = $vals2[ $i ];
- }
-
- Maasha::Biopieces::put_record( $record, $out );
- }
-}
-
-
sub script_sort_records
{
# Martin A. Hansen, August 2007.
projects / biopieces.git / commitdiff