# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $options, $in, $out, $record, $contig_hash, $i, $s_id, $strand, $new_record, $contig, $beg, $end, @array, $min, $max, $mean );
+my ( $options, $in, $out, $record, $contig_hash, $i, $s_id, $q_id, $strand, $new_record, $contig, $beg, $end, @array, $min, $max, $mean );
$options = Maasha::Biopieces::parse_options(
[
+ { long => 'q_id', short => 'q', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
{ long => 'strand', short => 's', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
{ long => 'bridge', short => 'b', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
]
{
if ( $record->{ 'S_ID' } and $record->{ 'STRAND' } )
{
+ if ( $options->{ 'q_id' } ) {
+ next if not $record->{ 'Q_ID' };
+ } else {
+ $record->{ 'Q_ID' } = 'X';
+ }
+
if ( $options->{ 'strand' } ) {
next if not $record->{ 'STRAND' };
} else {
$record->{ 'STRAND' } = 'X';
}
- if ( $record->{ 'Q_ID' } and $record->{ 'S_BEG' } and $record->{ 'S_END' } )
+ if ( defined $record->{ 'S_BEG' } and defined $record->{ 'S_END' } )
{
for ( $i = $record->{ 'S_BEG' }; $i <= $record->{ 'S_END' }; $i++ ) {
- $contig_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'STRAND' } }->[ $i ]++;
+ $contig_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'Q_ID' } }->{ $record->{ 'STRAND' } }->[ $i ]++;
}
}
- if ( $record->{ 'Q_ID1' } and $record->{ 'S_BEG1' } and $record->{ 'S_END1' } and
- $record->{ 'Q_ID2' } and $record->{ 'S_BEG2' } and $record->{ 'S_END2' }
- )
+ if ( defined $record->{ 'S_BEG1' } and defined $record->{ 'S_END1' } and
+ defined $record->{ 'S_BEG2' } and defined $record->{ 'S_END2' } )
{
if ( $options->{ 'bridge' } )
{
( $record->{ 'S_BEG1' }, $record->{ 'S_END2' } ) = ( $record->{ 'S_BEG2' }, $record->{ 'S_END1' } ) if ( $record->{ 'S_BEG1' } > $record->{ 'S_END2' } );
for ( $i = $record->{ 'S_BEG1' }; $i <= $record->{ 'S_END2' }; $i++ ) {
- $contig_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'STRAND' } }->[ $i ]++;
+ $contig_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'Q_ID' } }->{ $record->{ 'STRAND' } }->[ $i ]++;
}
}
else
{
for ( $i = $record->{ 'S_BEG1' }; $i <= $record->{ 'S_END1' }; $i++ ) {
- $contig_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'STRAND' } }->[ $i ]++;
+ $contig_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'Q_ID' } }->{ $record->{ 'STRAND' } }->[ $i ]++;
}
for ( $i = $record->{ 'S_BEG2' }; $i <= $record->{ 'S_END2' }; $i++ ) {
- $contig_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'STRAND' } }->[ $i ]++;
+ $contig_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'Q_ID' } }->{ $record->{ 'STRAND' } }->[ $i ]++;
}
}
}
foreach $s_id ( keys %{ $contig_hash } )
{
- foreach $strand ( keys %{ $contig_hash->{ $s_id } } )
+ foreach $q_id ( keys %{ $contig_hash->{ $s_id } } )
{
- $beg = 0;
- $end = 0;
-
- while ( ( $beg, $end ) = Maasha::UCSC::Wiggle::fixedstep_scan( $contig_hash->{ $s_id }->{ $strand }, $beg ) )
+ foreach $strand ( keys %{ $contig_hash->{ $s_id }->{ $q_id } } )
{
- @array = @{ $contig_hash->{ $s_id }->{ $strand } }[ $beg .. $end - 1 ];
-
- ( $min, $max ) = Maasha::Calc::minmax( \@array );
- $mean = Maasha::Calc::mean( \@array );
-
- $new_record->{ 'S_ID' } = $s_id;
- $new_record->{ 'STRAND' } = $strand if $options->{ 'strand' };
- $new_record->{ 'S_BEG' } = $beg;
- $new_record->{ 'S_END' } = $end;
- $new_record->{ 'CONTIG_ID' } = $contig;
- $new_record->{ 'CONTIG_LEN' } = $end - $beg + 1;
- $new_record->{ 'CONTIG_MIN' } = $min;
- $new_record->{ 'CONTIG_MAX' } = $max;
- $new_record->{ 'CONTIG_MEAN' } = sprintf "%.2f", $mean;
- $new_record->{ 'CONTIG' } = join ( ";", @array );
-
- $beg = $end + 1;
- $contig++;
-
- Maasha::Biopieces::put_record( $new_record, $out );
+ $beg = 0;
+ $end = 0;
+
+ while ( ( $beg, $end ) = Maasha::UCSC::Wiggle::fixedstep_scan( $contig_hash->{ $s_id }->{ $q_id }->{ $strand }, $beg ) )
+ {
+ @array = @{ $contig_hash->{ $s_id }->{ $q_id }->{ $strand } }[ $beg .. $end - 1 ];
+
+ ( $min, $max ) = Maasha::Calc::minmax( \@array );
+ $mean = Maasha::Calc::mean( \@array );
+
+ $new_record->{ 'S_ID' } = $s_id;
+ $new_record->{ 'Q_ID' } = $q_id if $options->{ 'q_id' };
+ $new_record->{ 'STRAND' } = $strand if $options->{ 'strand' };
+ $new_record->{ 'S_BEG' } = $beg;
+ $new_record->{ 'S_END' } = $end;
+ $new_record->{ 'CONTIG_ID' } = $contig;
+ $new_record->{ 'CONTIG_LEN' } = $end - $beg + 1;
+ $new_record->{ 'CONTIG_MIN' } = $min;
+ $new_record->{ 'CONTIG_MAX' } = $max;
+ $new_record->{ 'CONTIG_MEAN' } = sprintf "%.2f", $mean;
+ $new_record->{ 'CONTIG' } = join ( ";", @array );
+
+ $beg = $end + 1;
+ $contig++;
+
+ Maasha::Biopieces::put_record( $new_record, $out );
+ }
}
}
}