elsif ( $script eq "assemble_tag_contigs" ) { script_assemble_tag_contigs( $in, $out, $options ) }
elsif ( $script eq "length_seq" ) { script_length_seq( $in, $out, $options ) }
elsif ( $script eq "uppercase_seq" ) { script_uppercase_seq( $in, $out, $options ) }
- elsif ( $script eq "shuffle_seq" ) { script_shuffle_seq( $in, $out, $options ) }
elsif ( $script eq "analyze_seq" ) { script_analyze_seq( $in, $out, $options ) }
elsif ( $script eq "analyze_tags" ) { script_analyze_tags( $in, $out, $options ) }
elsif ( $script eq "complexity_seq" ) { script_complexity_seq( $in, $out, $options ) }
elsif ( $script eq "fold_seq" ) { script_fold_seq( $in, $out, $options ) }
elsif ( $script eq "split_seq" ) { script_split_seq( $in, $out, $options ) }
elsif ( $script eq "split_bed" ) { script_split_bed( $in, $out, $options ) }
- elsif ( $script eq "align_seq" ) { script_align_seq( $in, $out, $options ) }
elsif ( $script eq "tile_seq" ) { script_tile_seq( $in, $out, $options ) }
elsif ( $script eq "invert_align" ) { script_invert_align( $in, $out, $options ) }
elsif ( $script eq "patscan_seq" ) { script_patscan_seq( $in, $out, $options ) }
elsif ( $script eq "merge_records" ) { script_merge_records( $in, $out, $options ) }
elsif ( $script eq "compute" ) { script_compute( $in, $out, $options ) }
elsif ( $script eq "flip_tab" ) { script_flip_tab( $in, $out, $options ) }
- elsif ( $script eq "add_ident" ) { script_add_ident( $in, $out, $options ) }
elsif ( $script eq "count_records" ) { script_count_records( $in, $out, $options ) }
elsif ( $script eq "random_records" ) { script_random_records( $in, $out, $options ) }
elsif ( $script eq "sort_records" ) { script_sort_records( $in, $out, $options ) }
eval|e=s
);
}
- elsif ( $script eq "add_ident" )
- {
- @options = qw(
- prefix|p=s
- key|k=s
- );
- }
elsif ( $script eq "count_records" )
{
@options = qw(
}
-sub script_shuffle_seq
-{
- # Martin A. Hansen, December 2007.
-
- # Shuffle sequences in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- ) = @_;
-
- # Returns nothing.
-
- my ( $record );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- $record->{ "SEQ" } = Maasha::Seq::seq_shuffle( $record->{ "SEQ" } ) if $record->{ "SEQ" };
-
- Maasha::Biopieces::put_record( $record, $out );
- }
-}
-
-
sub script_analyze_seq
{
# Martin A. Hansen, August 2007.
}
-sub script_align_seq
-{
- # Martin A. Hansen, August 2007.
-
- # Align sequences in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, @entries, $entry );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
- push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
- } elsif ( $record->{ "Q_ID" } and $record->{ "SEQ" } ) {
- push @entries, [ $record->{ "Q_ID" }, $record->{ "SEQ" } ];
- } else {
- Maasha::Biopieces::put_record( $record, $out );
- }
- }
-
- @entries = Maasha::Align::align( \@entries );
-
- foreach $entry ( @entries )
- {
- if ( $entry->[ SEQ_NAME ] and $entry->[ SEQ ] )
- {
- $record = {
- SEQ_NAME => $entry->[ SEQ_NAME ],
- SEQ => $entry->[ SEQ ],
- };
-
- Maasha::Biopieces::put_record( $record, $out );
- }
- }
-}
-
-
sub script_tile_seq
{
# Martin A. Hansen, February 2008.
}
-sub script_add_ident
-{
- # Martin A. Hansen, May 2008.
-
- # Add a unique identifier to each record in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $key, $prefix, $i );
-
- $key = $options->{ "key" } || "ID";
- $prefix = $options->{ "prefix" } || "ID";
-
- $i = 0;
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- $record->{ $key } = sprintf( "$prefix%08d", $i );
-
- Maasha::Biopieces::put_record( $record, $out );
-
- $i++;
- }
-}
-
-
sub script_count_records
{
# Martin A. Hansen, August 2007.