X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=code_perl%2FMaasha%2FBiopieces.pm;h=29a914a230ef1bccb22aa55409bc9fc06b55fb34;hb=7c9609e8a165301350118cde21387c8a2e63dd42;hp=06d4b3d8a02e9db84e287b9a92dcf71ecb23830e;hpb=e2ee381ee079a78605a6381d5545a741a99c34c8;p=biopieces.git

diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index 06d4b3d..29a914a 100644
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -51,6 +51,7 @@ use Maasha::NCBI;
 use Maasha::GFF;
 use Maasha::TwoBit;
 use Maasha::Solid;
+use Maasha::Solexa;
 use Maasha::SQL;
 use Maasha::Gwiki;
 
@@ -161,6 +162,8 @@ sub run_script
 
     $options = get_options( $script );
 
+    $options->{ "SCRIPT" } = $script;
+
     if ( $script ne "list_biopieces" and $script ne "list_genomes" ) {
         $script = "print_usage" if ( -t STDIN and keys %{ $options } <= 1 or $options->{ 'help' } );
     }
@@ -216,6 +219,7 @@ sub run_script
     elsif ( $script eq "create_blast_db" )          { script_create_blast_db(           $in, $out, $options ) }
     elsif ( $script eq "blast_seq" )                { script_blast_seq(                 $in, $out, $options ) }
     elsif ( $script eq "blat_seq" )                 { script_blat_seq(                  $in, $out, $options ) }
+    elsif ( $script eq "soap_seq" )                 { script_soap_seq(                  $in, $out, $options ) }
     elsif ( $script eq "match_seq" )                { script_match_seq(                 $in, $out, $options ) }
     elsif ( $script eq "create_vmatch_index" )      { script_create_vmatch_index(       $in, $out, $options ) }
     elsif ( $script eq "vmatch_seq" )               { script_vmatch_seq(                $in, $out, $options ) }
@@ -230,9 +234,11 @@ sub run_script
     elsif ( $script eq "write_solid" )              { script_write_solid(               $in, $out, $options ) }
     elsif ( $script eq "head_records" )             { script_head_records(              $in, $out, $options ) }
     elsif ( $script eq "remove_keys" )              { script_remove_keys(               $in, $out, $options ) }
+    elsif ( $script eq "remove_adaptor" )           { script_remove_adaptor(            $in, $out, $options ) }
     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 "grab" )                     { script_grab(                      $in, $out, $options ) }
     elsif ( $script eq "compute" )                  { script_compute(                   $in, $out, $options ) }
     elsif ( $script eq "flip_tab" )                 { script_flip_tab(                  $in, $out, $options ) }
@@ -260,9 +266,6 @@ sub run_script
 
     close $in if defined $in;
     close $out;
-
-    # unset status   - missing
-    # write log file - missing
 }
 
 
@@ -277,7 +280,7 @@ sub get_options
 
     # Returns hash
 
-    my ( %options, @options, $opt, @genomes );
+    my ( %options, @options, $opt, @genomes, $real );
 
     if ( $script eq "print_usage" )
     {
@@ -363,6 +366,7 @@ sub get_options
     {
         @options = qw(
             data_in|i=s
+            samples|s=s
             num|n=s
         );
     }
@@ -386,6 +390,7 @@ sub get_options
         @options = qw(
             data_in|i=s
             num|n=s
+            format|f=s
             quality|q=s
         );
     }
@@ -569,6 +574,17 @@ sub get_options
             ooc|c
         );
     }
+    elsif ( $script eq "soap_seq" )
+    {
+        @options = qw(
+            in_file|i=s
+            genome|g=s
+            seed_size|s=s
+            mismatches|m=s
+            gap_size|G=s
+            cpus|c=s
+        );
+    }
     elsif ( $script eq "match_seq" )
     {
         @options = qw(
@@ -718,6 +734,15 @@ sub get_options
             save_keys|K=s
         );
     }
+    elsif ( $script eq "remove_adaptor" )
+    {
+        @options = qw(
+            adaptor|a=s
+            mismatches|m=s
+            no_remove|n
+            offset|o=s
+        );
+    }
     elsif ( $script eq "rename_keys" )
     {
         @options = qw(
@@ -738,6 +763,13 @@ sub get_options
             delimit|d=s
         );
     }
+    elsif ( $script eq "merge_records" )
+    {
+        @options = qw(
+            keys|k=s
+            merge|m=s
+        );
+    }
     elsif ( $script eq "grab" )
     {
         @options = qw(
@@ -908,6 +940,8 @@ sub get_options
             use_score|u
             visibility|v=s
             wiggle|w
+            score|S
+            log10|L
             color|c=s
             chunk_size|C=s
         );
@@ -921,17 +955,15 @@ sub get_options
     );
 
 #    print STDERR Dumper( \@options );
-
+    
     GetOptions(
         \%options,
         @options,
     );
 
-    $options{ "script" } = $script;
-
 #    print STDERR Dumper( \%options );
 
-    if ( -t STDIN && scalar( keys %options ) == 1 or $options{ "help" } ) {
+    if ( -t STDIN && scalar( keys %options ) == 0 or $options{ "help" } ) {
         return wantarray ? %options : \%options;
     }
 
@@ -943,6 +975,7 @@ sub get_options
     $options{ "feats" }     = [ split ",", $options{ "feats" } ]     if defined $options{ "feats" };
     $options{ "frames" }    = [ split ",", $options{ "frames" } ]    if defined $options{ "frames" };
     $options{ "formats" }   = [ split ",", $options{ "formats" } ]   if defined $options{ "formats" };
+    $options{ "samples" }   = [ split ",", $options{ "samples" } ]   if defined $options{ "samples" };
     
     # ---- check arguments ----
 
@@ -955,7 +988,9 @@ sub get_options
 
     map { Maasha::Common::error( qq(Argument to --cols must be a whole numbers - not "$_") ) if $_ !~ /^\d+$/ } @{ $options{ "cols" } } if $options{ "cols" };
 
-#    print STDERR Dumper( \%options );
+    # print STDERR Dumper( \%options );
+
+    $real = "beg|end|word_size|wrap|chunk_size|tile_size|len|prefix_length|mismatches|offset|num|skip|cpus|window_size|step_size";
 
     foreach $opt ( keys %options )
     {
@@ -963,7 +998,7 @@ sub get_options
         {
             Maasha::Common::error( qq(Argument to --$opt must be a valid file or fileglob expression - not "$options{ $opt }") );
         }
-        elsif ( $opt =~ /beg|end|word_size|wrap|chunk_size|tile_size|len|prefix_length|num|skip|cpus|window_size|step_size/ and $options{ $opt } !~ /^\d+$/ )
+        elsif ( $opt =~ /$real/ and $options{ $opt } !~ /^\d+$/ )
         {
             Maasha::Common::error( qq(Argument to --$opt must be a whole number - not "$options{ $opt }") );
         }
@@ -992,13 +1027,21 @@ sub get_options
                 Maasha::Common::error( qq(Genome $options{ $opt } not found in "$ENV{ 'BP_DATA' }/genomes/") );
             }
         }
-        elsif ( $opt eq "terminal" and not $options{ $opt } =~ /^(svg|post|dumb)/ )
+        elsif ( $opt eq "terminal" and not $options{ $opt } =~ /^(svg|post|dumb|x11)/ )
         {
             Maasha::Common::error( qq(Bad --$opt argument "$options{ $opt }") );
         }
-        elsif ( $opt eq "table" and $options{ $opt } =~ /-\./ )
+        elsif ( $opt eq "table" and $options{ $opt } =~ /(-|\.)/ )
         {
-            Maasha::Common::error( qq(Character '$options{ $opt }' is not allowed in table names) );
+            Maasha::Common::error( qq(Character '$1' is not allowed in table name: $options{ $opt }) );
+        }
+        elsif ( $opt eq "merge" and $options{ $opt } !~ /^(AandB|AorB|BorA|AnotB|BnotA)$/ )
+        {
+            Maasha::Common::error( qq(Argument to --$opt must be AandB, AorB, BorA, AnotB, or BnotA - not "$options{ $opt }") );
+        }
+        elsif ( $opt eq "format" and $script eq "read_solexa" and $options{ $opt } !~ /octal|decimal/ )
+        {
+            Maasha::Common::error( qq(Argument to --$opt must be octal or decimal - not "$options{ $opt }") );
         }
     }
 
@@ -1007,7 +1050,9 @@ sub get_options
     Maasha::Common::error( qq(no --database or --genome specified) )    if $script eq "blast_seq" and not $options{ "genome" } and not $options{ "database" };
     Maasha::Common::error( qq(both --database and --genome specified) ) if $script eq "blast_seq" and $options{ "genome" } and $options{ "database" };
     Maasha::Common::error( qq(no --index_name or --genome specified) )  if $script eq "vmatch_seq" and not $options{ "genome" } and not $options{ "index_name" };
-    Maasha::Common::error( qq(both --index and --genome specified) )    if $script eq "vmatch_seq" and $options{ "genome" } and $options{ "index" };
+    Maasha::Common::error( qq(both --index and --genome specified) )    if $script eq "vmatch_seq" and $options{ "genome" } and $options{ "index_name" };
+    Maasha::Common::error( qq(no --in_file or --genome specified) )     if $script eq "soap_seq" and not $options{ "genome" } and not $options{ "in_file" };
+    Maasha::Common::error( qq(both --in_file and --genome specified) )  if $script eq "soap_seq" and $options{ "genome" } and $options{ "in_file" };
     Maasha::Common::error( qq(no --genome specified) )                  if $script =~ /format_genome|get_genome_seq|get_genome_align|get_genome_phastcons|blat_seq|plot_phastcons_profiles|plot_karyogram/ and not $options{ "genome" };
     Maasha::Common::error( qq(no --key specified) )                     if $script =~ /plot_lendist|plot_histogram/ and not $options{ "key" };
     Maasha::Common::error( qq(no --keys speficied) )                    if $script =~ /sort_records|count_vals|sum_vals|mean_vals|median_vals|length_vals/ and not $options{ "keys" };
@@ -1044,7 +1089,7 @@ sub script_print_usage
     if ( $options->{ 'data_in' } ) {
         $file = $options->{ 'data_in' };
     } else {
-        $file = join "", $ENV{ 'BP_DIR' }, "/bp_usage/", $options->{ 'script' }, ".wiki";
+        $file = join "", $ENV{ 'BP_DIR' }, "/bp_usage/", $options->{ 'SCRIPT' }, ".wiki";
     }
 
     $wiki = Maasha::Gwiki::gwiki_read( $file );
@@ -1090,6 +1135,7 @@ sub script_list_biopieces
             @{ $wiki } = grep { $_->[ 0 ]->{ 'FORMAT' }  =~ /paragraph/ } @{ $wiki };
 
             $synopsis = $wiki->[ 0 ]->[ 0 ]->{ 'TEXT' };
+            $synopsis =~ s/!(\w)/$1/g;
 
             printf( "%-30s%s\n", $program, $synopsis );
         }
@@ -1298,7 +1344,7 @@ sub script_read_psl
 
     # Returns nothing.
 
-    my ( $record, @files, $file, $entries, $entry, $num );
+    my ( $record, $file, $data_in, $num );
 
     while ( $record = get_record( $in ) ) {
         put_record( $record, $out );
@@ -1308,11 +1354,11 @@ sub script_read_psl
 
     foreach $file ( @{ $options->{ "files" } } )
     {
-        $entries = Maasha::UCSC::psl_get_entries( $file );
+        $data_in = Maasha::Common::read_open( $file );
 
-        foreach $entry ( @{ $entries } )
+        while ( $record = Maasha::UCSC::psl_get_entry( $data_in ) ) 
         {
-            put_record( $entry, $out );
+            put_record( $record, $out );
 
             goto NUM if $options->{ "num" } and $num == $options->{ "num" };
 
@@ -1398,10 +1444,11 @@ sub script_read_fixedstep
 
             if ( $head =~ /^chrom=([^ ]+) start=(\d+) step=(\d+)$/ )
             {
-                $record->{ "CHR" }     = $1;
-                $record->{ "CHR_BEG" } = $2;
-                $record->{ "STEP" }    = $3;
-                $record->{ "VALS" }    = join ",", @{ $entry };
+                $record->{ "REC_TYPE" } = "fixed_step";
+                $record->{ "CHR" }      = $1;
+                $record->{ "CHR_BEG" }  = $2;
+                $record->{ "STEP" }     = $3;
+                $record->{ "VALS" }     = join ",", @{ $entry };
             }
 
             put_record( $record, $out );
@@ -1706,7 +1753,7 @@ sub script_read_soft
 
     # Returns nothing.
 
-    my ( $data_in, $file, $num, $records, $record, $soft_index, $fh, @platforms, $plat_table, @samples, $sample, $old_end );
+    my ( $data_in, $file, $num, $records, $record, $soft_index, $fh, @platforms, $plat_table, @samples, $sample, $old_end, $skip );
 
     while ( $record = get_record( $in ) ) {
         put_record( $record, $out );
@@ -1716,21 +1763,30 @@ sub script_read_soft
 
     foreach $file ( @{ $options->{ "files" } } )
     {
+        print STDERR "Creating index for file: $file\n" if $options->{ "verbose" };
+
         $soft_index = Maasha::NCBI::soft_index_file( $file );
 
         $fh         = Maasha::Common::read_open( $file );
 
-        @platforms  = grep { $_->[ 0 ] =~ /PLATFORM/ } @{ $soft_index };
+        @platforms  = grep { $_->{ "SECTION" } =~ /PLATFORM/ } @{ $soft_index };
+
+        print STDERR "Getting platform tables for file: $file\n" if $options->{ "verbose" };
 
-        $plat_table = Maasha::NCBI::soft_get_platform( $fh, $platforms[ 0 ]->[ 1 ], $platforms[ -1 ]->[ 2 ] );
+        $plat_table = Maasha::NCBI::soft_get_platform( $fh, $platforms[ 0 ]->{ "LINE_BEG" }, $platforms[ -1 ]->{ "LINE_END" } );
 
-        @samples    = grep { $_->[ 0 ] =~ /SAMPLE/ } @{ $soft_index };
+        @samples    = grep { $_->{ "SECTION" } =~ /SAMPLE/ } @{ $soft_index };
 
-        $old_end    = $platforms[ -1 ]->[ 2 ];
+        $old_end    = $platforms[ -1 ]->{ "LINE_END" };
 
         foreach $sample ( @samples )
         {
-            $records = Maasha::NCBI::soft_get_sample( $fh, $plat_table, $sample->[ 1 ] - $old_end - 1, $sample->[ 2 ] - $old_end - 1 );
+            $skip = 0;
+            $skip = 1 if ( $options->{ "samples" } and grep { $sample->{ "SECTION" } !~ /$_/ } @{ $options->{ "samples" } } );
+
+            print STDERR "Getting samples for dataset: $sample->{ 'SECTION' }\n" if $options->{ "verbose" } and not $skip;
+
+            $records = Maasha::NCBI::soft_get_sample( $fh, $plat_table, $sample->{ "LINE_BEG" } - $old_end - 1, $sample->{ "LINE_END" } - $old_end - 1, $skip );
 
             foreach $record ( @{ $records } )
             {
@@ -1741,7 +1797,7 @@ sub script_read_soft
                 $num++;
             }
 
-            $old_end = $sample->[ 2 ];
+            $old_end = $sample->{ "LINE_END" };
         }
 
         close $fh;
@@ -1862,8 +1918,9 @@ sub script_read_solexa
 
     # Returns nothing.
 
-    my ( $record, $file, $base_name, $data_in, $line, $num, @fields, @seqs, @scores, $i, $seq, $seq_count );
+    my ( $record, $file, $data_in, $entry, $num, @seqs, @scores, $i );
 
+    $options->{ "format" }  ||= "octal";
     $options->{ "quality" } ||= 20;
 
     while ( $record = get_record( $in ) ) {
@@ -1874,35 +1931,33 @@ sub script_read_solexa
 
     foreach $file ( @{ $options->{ "files" } } )
     {
-        $data_in   = Maasha::Common::read_open( $file );
-        $base_name = Maasha::Common::get_basename( $file );
-        $base_name =~ s/\..*//;
-
-        $seq_count = 0;
+        $data_in = Maasha::Common::read_open( $file );
 
-        while ( $line = <$data_in> )
+        if ( $options->{ "format" } eq "octal" )
         {
-            @fields = split /:/, $line;
-            @seqs   = split //, $fields[ 5 ];
-            @scores = split / /, $fields[ -1 ];
+            while ( $entry = Maasha::Solexa::solexa_get_entry_octal( $data_in ) )
+            {
+                $record = Maasha::Solexa::solexa2biopiece( $entry, $options->{ "quality" } );
 
-            for ( $i = 0; $i < @scores; $i++ ) {
-                $seqs[ $i ] = lc $seqs[ $i ] if $scores[ $i ] < $options->{ "quality" };
-            }
+                put_record( $record, $out );
 
-            $seq = join "", @seqs;
+                goto NUM if $options->{ "num" } and $num == $options->{ "num" };
 
-            $record->{ "SEQ_NAME" }     = sprintf( "%s_ID%08d", $base_name, $seq_count );
-            $record->{ "SEQ" }          = $seq;
-            $record->{ "SEQ_LEN" }      = length $seq;
-            $record->{ "SCORE_MEAN" }   = sprintf ( "%.2f", Maasha::Calc::mean( \@scores ) );
+                $num++;
+            }
+        }
+        else
+        {
+            while ( $entry = Maasha::Solexa::solexa_get_entry_decimal( $data_in ) )
+            {
+                $record = Maasha::Solexa::solexa2biopiece( $entry, $options->{ "quality" } );
 
-            put_record( $record, $out );
+                put_record( $record, $out );
 
-            goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+                goto NUM if $options->{ "num" } and $num == $options->{ "num" };
 
-            $seq_count++;
-            $num++;
+                $num++;
+            }
         }
 
         close $data_in;
@@ -2024,7 +2079,7 @@ sub script_format_genome
 
     # Returns nothing.
 
-    my ( $dir, $genome, $fasta_dir, $phastcons_dir, $vals, $fh_out, $record, $format, $index );
+    my ( $dir, $genome, $fasta_dir, $phastcons_dir, $vals, $fh_out, $record, $format, $index, $entry );
 
     $dir    = $options->{ 'dir' } || $ENV{ 'BP_DATA' };
     $genome = $options->{ 'genome' };
@@ -2059,9 +2114,9 @@ sub script_format_genome
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $fh_out and $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+        if ( $fh_out and $entry = record2fasta( $record ) )
         {
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_out, $options->{ "wrap" } );
+            Maasha::Fasta::put_entry( $entry, $fh_out, $options->{ "wrap" } );
         }
         elsif ( $fh_out and $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "STEP" } and $record->{ "VALS" } )
         {
@@ -3283,8 +3338,6 @@ sub script_patscan_seq
 
             $i++;
         }
-
-#        put_record( $record, $out );
     }
 
     close $fh_out;
@@ -3354,7 +3407,7 @@ sub script_create_blast_db
 
     # Returns nothing.
 
-    my ( $fh, $seq_type, $path, $record );
+    my ( $fh, $seq_type, $path, $record, $entry );
 
     $path = $options->{ "database" };
 
@@ -3364,11 +3417,11 @@ sub script_create_blast_db
     {
         put_record( $record, $out ) if not $options->{ "no_stream" };
 
-        if ( $record->{ "SEQ" } and $record->{ "SEQ_NAME" } )
+        if ( $entry = record2fasta( $record ) )
         {
-            $seq_type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $seq_type;
+            $seq_type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not $seq_type;
 
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh );
+            Maasha::Fasta::put_entry( $entry, $fh );
         }
     }
 
@@ -3397,14 +3450,14 @@ sub script_blast_seq
 
     # Returns nothing.
 
-    my ( $genome, $q_type, $s_type, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $line, @fields );
+    my ( $genome, $q_type, $s_type, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $line, @fields, $entry );
 
     $options->{ "e_val" }  = 10 if not defined $options->{ "e_val" };
     $options->{ "filter" } = "F";
     $options->{ "filter" } = "T" if $options->{ "filter" };
     $options->{ "cpus" } ||= 1;
 
-    $options->{ "database" } = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/blast/$options->{ 'genome' }.fna"if $options->{ 'genome' };
+    $options->{ "database" } = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/blast/$options->{ 'genome' }.fna" if $options->{ 'genome' };
 
     $tmp_in  = "$BP_TMP/blast_query.seq";
     $tmp_out = "$BP_TMP/blast.result";
@@ -3413,11 +3466,11 @@ sub script_blast_seq
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+        if ( $entry = record2fasta( $record ) )
         {
-            $q_type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $q_type;
+            $q_type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not $q_type;
 
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_out );
+            Maasha::Fasta::put_entry( $entry, $fh_out );
         }
 
         put_record( $record, $out );
@@ -3444,7 +3497,41 @@ sub script_blast_seq
         }
     }
 
-    Maasha::Common::run( "blastall", "-p $options->{ 'program' } -e $options->{ 'e_val' } -a $options->{ 'cpus' } -m 8 -i $tmp_in -d $options->{ 'database' } -F $options->{ 'filter' } -o $tmp_out > /dev/null 2>&1", 1 );
+    if ( $options->{ 'verbose' } )
+    {
+        Maasha::Common::run(
+            "blastall",
+            join( " ",
+                "-p $options->{ 'program' }",
+                "-e $options->{ 'e_val' }",
+                "-a $options->{ 'cpus' }",
+                "-m 8",
+                "-i $tmp_in",
+                "-d $options->{ 'database' }",
+                "-F $options->{ 'filter' }",
+                "-o $tmp_out",
+            ),
+            1
+        );
+    }
+    else
+    {
+        Maasha::Common::run(
+            "blastall",
+            join( " ",
+                "-p $options->{ 'program' }",
+                "-e $options->{ 'e_val' }",
+                "-a $options->{ 'cpus' }",
+                "-m 8",
+                "-i $tmp_in",
+                "-d $options->{ 'database' }",
+                "-F $options->{ 'filter' }",
+                "-o $tmp_out",
+                "> /dev/null 2>&1"
+            ),
+            1
+        );
+    }
 
     unlink $tmp_in;
 
@@ -3507,7 +3594,7 @@ sub script_blat_seq
 
     # Returns nothing.
 
-    my ( $blat_args, $genome_file, $query_file, $fh_in, $fh_out, $type, $record, $result_file, $entries );
+    my ( $blat_args, $genome_file, $query_file, $fh_in, $fh_out, $type, $record, $result_file, $entries, $entry );
 
     $genome_file = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna";
 
@@ -3530,10 +3617,10 @@ sub script_blat_seq
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+        if ( $entry = record2fasta( $record ) )
         {
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_out, 80 );
-            $type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
+            $type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not $type;
+            Maasha::Fasta::put_entry( $entry, $fh_out, 80 );
         }
 
         put_record( $record, $out );
@@ -3558,6 +3645,98 @@ sub script_blat_seq
 }
 
 
+sub script_soap_seq
+{
+    # Martin A. Hansen, July 2008.
+
+    # soap sequences in stream against a given file or genome.
+
+    my ( $in,        # handle to in stream
+         $out,       # handle to out stream
+         $options,   # options hash
+       ) = @_;
+
+    # Returns nothing.
+
+    my ( $genome, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $line, @fields, $entry, $count, $args );
+
+    $options->{ "seed_size" }  ||= 10;
+    $options->{ "mismatches" } ||= 2;
+    $options->{ "gap_size" }   ||= 0;
+    $options->{ "cpus" }       ||= 1;
+
+    if ( $options->{ "genome" } ) {
+        $options->{ "in_file" } = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna";
+    }
+
+    $tmp_in  = "$BP_TMP/soap_query.seq";
+    $tmp_out = "$BP_TMP/soap.result";
+
+    $fh_out = Maasha::Common::write_open( $tmp_in );
+ 
+    $count = 0;
+
+    while ( $record = get_record( $in ) ) 
+    {
+        if ( $entry = record2fasta( $record ) )
+        {
+            Maasha::Fasta::put_entry( $entry, $fh_out );
+
+            $count++;
+        }
+
+        put_record( $record, $out );
+    }
+
+    close $fh_out;
+
+    if ( $count > 0 )
+    {
+        $args = join( " ",
+            "-s $options->{ 'seed_size' }",
+            "-r 2",
+            "-a $tmp_in",
+            "-v $options->{ 'mismatches' }",
+            "-g $options->{ 'gap_size' }",
+            "-p $options->{ 'cpus' }",
+            "-d $options->{ 'in_file' }",
+            "-o $tmp_out",
+        );
+
+        $args .= " > /dev/null 2>&1" if not $options->{ 'verbose' };
+
+        Maasha::Common::run( "soap", $args, 1 );
+
+        unlink $tmp_in;
+
+        $fh_out = Maasha::Common::read_open( $tmp_out );
+
+        undef $record;
+
+        while ( $line = <$fh_out> )
+        {
+            chomp $line;
+
+            @fields = split /\t/, $line;
+
+            $record->{ "REC_TYPE" }   = "SOAP";
+            $record->{ "Q_ID" }       = $fields[ 0 ];
+            $record->{ "SCORE" }      = $fields[ 3 ];
+            $record->{ "STRAND" }     = $fields[ 6 ];
+            $record->{ "S_ID" }       = $fields[ 7 ];
+            $record->{ "S_BEG" }      = $fields[ 8 ] - 1; # soap is 1-based
+            $record->{ "S_END" }      = $fields[ 8 ] + $fields[ 5 ] - 2;
+
+            put_record( $record, $out );
+        }
+
+        close $fh_out;
+    }
+
+    unlink $tmp_out;
+}
+
+
 sub script_match_seq
 {
     # Martin A. Hansen, August 2007.
@@ -3613,7 +3792,7 @@ sub script_create_vmatch_index
 
     # Returns nothing.
 
-    my ( $record, $file_tmp, $fh_tmp, $type );
+    my ( $record, $file_tmp, $fh_tmp, $type, $entry );
 
     if ( $options->{ "index_name" } )
     {
@@ -3623,11 +3802,11 @@ sub script_create_vmatch_index
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $options->{ "index_name" } and $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+        if ( $options->{ "index_name" } and $entry = record2fasta( $record ) )
         {
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_tmp );
+            Maasha::Fasta::put_entry( $entry, $fh_tmp );
 
-            $type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
+            $type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not defined $type;
         }
 
         put_record( $record, $out ) if not $options->{ "no_stream" };
@@ -3714,14 +3893,14 @@ sub script_write_fasta
 
     # Returns nothing.
 
-    my ( $record, $fh );
+    my ( $record, $fh, $entry );
 
     $fh = write_stream( $options->{ "data_out" }, $options->{ "compress" } );
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh, $options->{ "wrap" } );
+        if ( $entry = record2fasta( $record ) ) {
+            Maasha::Fasta::put_entry( $entry, $fh, $options->{ "wrap" } );
         }
 
         put_record( $record, $out ) if not $options->{ "no_stream" };
@@ -3953,6 +4132,17 @@ sub script_write_bed
 
             Maasha::UCSC::bed_put_entry( $new_record, $fh, 6 );
         }
+        elsif ( $record->{ "REC_TYPE" } eq "SOAP" and $record->{ "S_ID" } =~ /^chr/i )    # ---- Hits from Vmatch ----
+        {
+            $new_record->{ "CHR" }     = $record->{ "S_ID" };
+            $new_record->{ "CHR_BEG" } = $record->{ "S_BEG" };
+            $new_record->{ "CHR_END" } = $record->{ "S_END" };
+            $new_record->{ "Q_ID" }    = $record->{ "Q_ID" };
+            $new_record->{ "SCORE" }   = $record->{ "SCORE" } || 999;
+            $new_record->{ "STRAND" }  = $record->{ "STRAND" };
+
+            Maasha::UCSC::bed_put_entry( $new_record, $fh, 6 );
+        }
         elsif ( $record->{ "CHR" } and defined $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )  # ---- Generic data from tables ----
         {
             Maasha::UCSC::bed_put_entry( $record, $fh );
@@ -4050,7 +4240,7 @@ sub script_write_2bit
 
     # Returns nothing.
 
-    my ( $record, $mask, $tmp_file, $fh_tmp, $fh_in, $fh_out );
+    my ( $record, $mask, $tmp_file, $fh_tmp, $fh_in, $fh_out, $entry );
 
     $mask = 1 if not $options->{ "no_mask" };
 
@@ -4061,8 +4251,8 @@ sub script_write_2bit
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_tmp );
+        if ( $entry = record2fasta( $record ) ) {
+            Maasha::Fasta::put_entry( $entry, $fh_tmp );
         }
 
         put_record( $record, $out ) if not $options->{ "no_stream" };
@@ -4094,17 +4284,17 @@ sub script_write_solid
 
     # Returns nothing.
 
-    my ( $record, $fh, $seq_cs );
+    my ( $record, $fh, $entry );
 
     $fh = write_stream( $options->{ "data_out" }, $options->{ "compress" } );
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+        if ( $entry = record2fasta( $record ) )
         {
-            $seq_cs = Maasha::Solid::seq2color_space( uc $record->{ "SEQ" } );
+            $entry->[ SEQ ] = Maasha::Solid::seq2color_space( uc $entry->[ SEQ ] );
 
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $seq_cs ], $fh, $options->{ "wrap" } );
+            Maasha::Fasta::put_entry( $entry, $fh, $options->{ "wrap" } );
         }
 
         put_record( $record, $out ) if not $options->{ "no_stream" };
@@ -4376,6 +4566,57 @@ sub script_remove_keys
 }
 
 
+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 );
+
+    $max_mismatch = $options->{ "mismatches" } || 0;
+    $offset       = $options->{ "offset" }     || 15;
+    $adaptor      = $options->{ "adaptor" };
+    $adaptor_len  = length $adaptor;
+    $adaptor      = [ split //, uc $adaptor ];
+
+    $max_match    = $adaptor_len - $max_mismatch;
+
+    while ( $record = get_record( $in ) ) 
+    {
+        if ( $record->{ "SEQ" } )
+        {
+            $seq     = $record->{ "SEQ" };
+            $seq_len = length $seq;
+            $seq     = [ split //, uc $seq ];
+
+            $pos = Maasha::Seq::find_adaptor( $adaptor, $seq, $adaptor_len, $seq_len, $offset, $max_match, $max_mismatch );
+
+            $record->{ "ADAPTOR_POS" } = $pos;
+
+            if ( $pos >= 0 and not $options->{ "no_remove" } )
+            {
+                $record->{ "SEQ" }     = substr $record->{ "SEQ" }, 0, $pos;
+                $record->{ "SEQ_LEN" } = $pos;
+            }
+
+            put_record( $record, $out );
+        }
+        else
+        {
+            put_record( $record, $out );
+        }
+    }
+}
+
+
 sub script_rename_keys
 {
     # Martin A. Hansen, August 2007.
@@ -4482,6 +4723,177 @@ sub script_merge_vals
 }
 
 
+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 = 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 ];
+                }
+
+                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 ];
+                }
+
+                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 ];
+                }
+            
+                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 ];
+        }
+
+        put_record( $record, $out );
+    }
+
+    if ( $num2 > 0 and $merge =~ /^(BorA|BnotA)$/ )
+    {
+        undef $record;
+
+        for ( $i = 0; $i < @keys2; $i++ ) {
+            $record->{ $keys2[ $i ] } = $vals2[ $i ];
+        }
+
+        put_record( $record, $out );
+    }
+}
+
+
 sub script_grab
 {
     # Martin A. Hansen, August 2007.
@@ -4830,7 +5242,7 @@ sub script_count_records
         }
     }
 
-    $result = { "count_records" => $count };
+    $result = { "RECORDS_COUNT" => $count };
 
     $fh = write_stream( $options->{ "data_out" } );
 
@@ -4977,6 +5389,7 @@ sub script_count_vals
 
     $fh_out   = Maasha::Common::write_open( $tmp_file );
 
+    $cache    = 0;
     $num      = 0;
 
     while ( $record = get_record( $in ) ) 
@@ -5003,7 +5416,7 @@ sub script_count_vals
 
     if ( $cache )
     {
-        $num      = 0;
+        $num   = 0;
 
         $fh_in = Maasha::Common::read_open( $tmp_file );
 
@@ -5499,6 +5912,8 @@ sub script_upload_to_ucsc
 
     # Calculate the mean of values of given keys.
 
+    # This routine has developed into the most ugly hack. Do something!
+
     my ( $in,        # handle to in stream
          $out,       # handle to out stream
          $options,   # options hash
@@ -5507,7 +5922,7 @@ sub script_upload_to_ucsc
     # Returns nothing.
 
     my ( $record, $file, $wib_file, $wig_file, $wib_dir, $fh_in, $fh_out, $i, $first, $format, $args, $type, $columns, $append, %fh_hash,
-         $chr, $beg, $end, $block, $line, $max, $beg_block, $entry, $q_id, $clones );
+         $chr, $beg, $end, $block, $line, $max, $beg_block, $entry, $q_id, $clones, $vals );
 
     $options->{ "short_label" } ||= $options->{ 'table' };
     $options->{ "long_label" }  ||= $options->{ 'table' };
@@ -5527,8 +5942,6 @@ sub script_upload_to_ucsc
 
     if ( $options->{ 'wiggle' } )
     {
-        $options->{ "visibility" } = "full";
-
         while ( $record = get_record( $in ) )
         {
             put_record( $record, $out ) if not $options->{ "no_stream" };
@@ -5563,7 +5976,9 @@ sub script_upload_to_ucsc
                 $end  = $entry->{ 'CHR_END' };
                 $q_id = $entry->{ 'Q_ID' };
                 
-                if ( $q_id =~ /_(\d+)$/ ) {
+                if ( $options->{ "score" } ) {
+                    $clones = $entry->{ 'SCORE' };
+                } elsif ( $q_id =~ /_(\d+)$/ ) {
                     $clones = $1;
                 } else {
                     $clones = 1;
@@ -5599,29 +6014,13 @@ sub script_upload_to_ucsc
 
             close $fh_in;
 
-            Maasha::UCSC::fixedstep_put_entry( $chr, $beg_block, $block, $fh_out );
+            Maasha::UCSC::fixedstep_put_entry( $chr, $beg_block, $block, $fh_out, $options->{ "log10" } );
 
             unlink "$BP_TMP/$chr";
         }
 
         close $fh_out;
 
-        $wig_file = "$options->{ 'table' }.wig";
-        $wib_file = "$options->{ 'table' }.wib";
-
-        $wib_dir  = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'database' }/wib";
-
-        Maasha::Common::dir_create_if_not_exists( $wib_dir );
-
-        # Maasha::Common::run( "wigEncode", "$file $wig_file $wib_file > /dev/null 2>&1" );
-
-        `cd $BP_TMP && wigEncode $file $wig_file $wib_file > /dev/null 2>&1`;
-        Maasha::Common::run( "mv", "$BP_TMP/$wib_file $wib_dir" );
-
-        unlink $file;
-
-        $file = $wig_file;
-
         $format = "WIGGLE";
     }
     else
@@ -5632,7 +6031,17 @@ sub script_upload_to_ucsc
         {
             put_record( $record, $out ) if not $options->{ "no_stream" };
 
-            if ( $record->{ "REC_TYPE" } eq "PSL" )
+            if ( $record->{ "REC_TYPE" } eq "fixed_step" )
+            {
+                $vals = $record->{ "VALS" };
+                $vals =~ tr/,/\n/;
+
+                print $fh_out "fixedStep chrom=$record->{ 'CHR' } start=$record->{ 'CHR_BEG' } step=$record->{ 'STEP' }\n";
+                print $fh_out "$vals\n";
+
+                $format = "WIGGLE" if not $format;
+            }
+            elsif ( $record->{ "REC_TYPE" } eq "PSL" )
             {
                 Maasha::UCSC::psl_put_header( $fh_out ) if $first;
                 Maasha::UCSC::psl_put_entry( $record, $fh_out );
@@ -5748,6 +6157,27 @@ sub script_upload_to_ucsc
         }
         elsif ( $format eq "WIGGLE" )
         {
+            $options->{ "visibility" } = "full";
+
+            $wig_file = "$options->{ 'table' }.wig";
+            $wib_file = "$options->{ 'table' }.wib";
+
+            $wib_dir  = "$ENV{ 'HOME' }/ucsc/wib";
+
+            Maasha::Common::dir_create_if_not_exists( $wib_dir );
+
+            if ( $options->{ 'verbose' } ) {
+                `cd $BP_TMP && wigEncode $file $wig_file $wib_file`;
+            } else {
+                `cd $BP_TMP && wigEncode $file $wig_file $wib_file > /dev/null 2>&1`;
+            }
+
+            Maasha::Common::run( "mv", "$BP_TMP/$wib_file $wib_dir" );
+
+            unlink $file;
+
+            $file = $wig_file;
+
             $type = "wig 0";
 
             Maasha::UCSC::wiggle_upload_to_ucsc( $BP_TMP, $wib_dir, $file, $options );
@@ -5763,6 +6193,32 @@ sub script_upload_to_ucsc
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+sub record2fasta
+{
+    # Martin A. Hansen, July 2008.
+
+    # Given a biopiece record converts it to a FASTA record.
+    # If no generic SEQ or SEQ_NAME is found, the Q_* and S_* are
+    # tried in that order.
+
+    my ( $record,    # record
+       ) = @_;
+
+    # Returns a tuple.
+
+    my ( $seq_name, $seq );
+
+    $seq_name = $record->{ "SEQ_NAME" } || $record->{ "Q_ID" }  || $record->{ "S_ID" };
+    $seq      = $record->{ "SEQ" }      || $record->{ "Q_SEQ" } || $record->{ "S_SEQ" };
+
+    if ( defined $seq_name and defined $seq ) {
+        return wantarray ? ( $seq_name, $seq ) : [ $seq_name, $seq ];
+    } else {
+        return;
+    }
+}
+
+
 sub read_stream
 {
     # Martin A. Hansen, July 2007.
@@ -5821,10 +6277,10 @@ sub get_record
     # Reads one record at a time and converts that record
     # to a Perl data structure (a hash) which is returned.
 
-    my ( $fh,
+    my ( $fh,   # handle to stream
        ) = @_;
 
-    # Returns data structure. 
+    # Returns a hash. 
 
     my ( $block, @lines, $line, $key, $value, %record );
 
@@ -5840,7 +6296,7 @@ sub get_record
 
     foreach $line ( @lines )
     {
-        ( $key, $value ) = split ": ", $line;
+        ( $key, $value ) = split ": ", $line, 2;
 
         $record{ $key } = $value;
     }
@@ -5940,69 +6396,63 @@ sub sig_handler
             print STDERR "\nProgram '$script' died->$sig"                       . "  -  Please wait for temporary data to be removed\n";
         }
 
-        # This is a really bad solution, potentially, anyone can include this module and set
-        # the BP_TMP to point at any dir and thus take out the machine !!!
-
-        Maasha::Common::dir_remove( $BP_TMP );
+        clean_tmp();
     }
 
     exit( 0 );
 }
 
 
-END
-{
-    # This is a really bad solution, potentially, anyone can include this module and set
-    # the BP_TMP to point at any dir and thus take out the machine !!!
-
-    Maasha::Common::dir_remove( $BP_TMP );
-}
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-1;
-
-__END__
-
-
-sub script_read_soft
+sub clean_tmp
 {
-    # Martin A. Hansen, December 2007.
-
-    # Read soft format.
-    # http://www.ncbi.nlm.nih.gov/geo/info/soft2.html
+    # Martin A. Hansen, July 2008.
 
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
+    # Cleans out any unused temporary files and direcotries in BP_TMP.
 
     # Returns nothing.
 
-    my ( $data_in, $file, $num, $records, $record );
+    my ( $tmpdir, @dirs, $curr_pid, $dir, $user, $sid, $pid );
 
-    while ( $record = get_record( $in ) ) {
-        put_record( $record, $out );
-    }
+    $tmpdir = $ENV{ 'BP_TMP' } || Maasha::Common::error( 'No BP_TMP variable in environment.' );
 
-    $num = 1;
+    $curr_pid = Maasha::Common::get_processid();
 
-    foreach $file ( @{ $options->{ "files" } } )
-    {
-        $records = Maasha::NCBI::soft_parse( $file );
+    @dirs = Maasha::Common::ls_dirs( $tmpdir );
 
-        foreach $record ( @{ $records } )
+    foreach $dir ( @dirs )
+    {
+        if ( $dir =~ /^$tmpdir\/(.+)_(\d+)_(\d+)_bp_tmp$/ )
         {
-            put_record( $record, $out );
-
-            goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+            $user = $1;
+            $sid  = $2;
+            $pid  = $3;
 
-            $num++;
+            if ( $user eq Maasha::Common::get_user() )
+            {
+                if ( not Maasha::Common::process_running( $pid ) )
+                {
+                    # print STDERR "Removing stale dir: $dir\n";
+                    Maasha::Common::dir_remove( $dir );
+                }
+                elsif ( $pid == $curr_pid )
+                {
+                    # print STDERR "Removing current dir: $dir\n";
+                    Maasha::Common::dir_remove( $dir );
+                }
+            }
         }
     }
+}
 
-    NUM:
 
-    close $data_in if $data_in;
+END
+{
+    clean_tmp();
 }
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+1;
+
+__END__