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 ) }
@options = qw(
in_file|i=s
genome|g=s
+ seed_size|s=s
mismatches|m=s
gap_size|G=s
cpus|c=s
delimit|d=s
);
}
+ elsif ( $script eq "merge_records" )
+ {
+ @options = qw(
+ keys|k=s
+ merge|m=s
+ );
+ }
elsif ( $script eq "grab" )
{
@options = qw(
{
Maasha::Common::error( qq(Character '$options{ $opt }' is not allowed in table names) );
}
+ 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 }") );
+ }
}
Maasha::Common::error( qq(no --database specified) ) if $script eq "create_blast_db" and not $options{ "database" };
# Returns nothing.
- my ( $genome, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $line, @fields, $entry );
+ 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;
- $options->{ "in_file" } = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna" if $options->{ 'genome' };
+ 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 ) ) {
+ if ( $entry = record2fasta( $record ) )
+ {
Maasha::Fasta::put_entry( $entry, $fh_out );
+
+ $count++;
}
put_record( $record, $out );
close $fh_out;
- Maasha::Common::run( "soap", "-r 2 -a $tmp_in -v $options->{ 'mismatches' } -g $options->{ 'gap_size' } -p $options->{ 'cpus' } -d $options->{ 'in_file' } -o $tmp_out > /dev/null 2>&1", 1 );
+ 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",
+ );
- unlink $tmp_in;
+ $args .= " > /dev/null 2>&1" if not $options->{ 'verbose' };
- $fh_out = Maasha::Common::read_open( $tmp_out );
+ Maasha::Common::run( "soap", $args, 1 );
- undef $record;
+ unlink $tmp_in;
- while ( $line = <$fh_out> )
- {
- chomp $line;
+ $fh_out = Maasha::Common::read_open( $tmp_out );
- @fields = split /\t/, $line;
+ undef $record;
- $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;
+ while ( $line = <$fh_out> )
+ {
+ chomp $line;
- put_record( $record, $out );
- }
+ @fields = split /\t/, $line;
- close $fh_out;
+ $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_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.
$fh_out = Maasha::Common::write_open( $tmp_file );
+ $cache = 0;
$num = 0;
while ( $record = get_record( $in ) )
if ( $cache )
{
- $num = 0;
+ $num = 0;
$fh_in = Maasha::Common::read_open( $tmp_file );
foreach $dir ( @dirs )
{
- if ( $dir =~ /(.+)_(\d+)_(\d+)_bp_tmp/ )
+ if ( $dir =~ /^$tmpdir\/(.+)_(\d+)_(\d+)_bp_tmp$/ )
{
$user = $1;
$sid = $2;
$pid = $3;
- if ( not Maasha::Common::process_running( $pid ) )
- {
- # print STDERR "Removing stale dir: $dir\n";
- Maasha::Common::dir_remove( $dir );
- }
- elsif ( $pid == $curr_pid )
+ if ( $user eq Maasha::Common::get_user() )
{
- # print STDERR "Removing current dir: $dir\n";
- Maasha::Common::dir_remove( $dir );
+ 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 );
+ }
}
}
}
projects / biopieces.git / blobdiff