$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
if ( $script eq "print_usage" ) { script_print_usage( $in, $out, $options ) }
- elsif ( $script eq "read_psl" ) { script_read_psl( $in, $out, $options ) }
elsif ( $script eq "read_stockholm" ) { script_read_stockholm( $in, $out, $options ) }
elsif ( $script eq "read_phastcons" ) { script_read_phastcons( $in, $out, $options ) }
- elsif ( $script eq "read_soft" ) { script_read_soft( $in, $out, $options ) }
- elsif ( $script eq "read_solexa" ) { script_read_solexa( $in, $out, $options ) }
elsif ( $script eq "read_solid" ) { script_read_solid( $in, $out, $options ) }
elsif ( $script eq "read_mysql" ) { script_read_mysql( $in, $out, $options ) }
elsif ( $script eq "uppercase_seq" ) { script_uppercase_seq( $in, $out, $options ) }
data_in|i=s
);
}
- elsif ( $script eq "read_psl" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- );
- }
elsif ( $script eq "read_stockholm" )
{
@options = qw(
gap|g=s
);
}
- elsif ( $script eq "read_soft" )
- {
- @options = qw(
- data_in|i=s
- samples|s=s
- num|n=s
- );
- }
- elsif ( $script eq "read_solexa" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- format|f=s
- quality|q=s
- );
- }
elsif ( $script eq "read_solid" )
{
@options = qw(
{
Maasha::Common::error( qq(Argument to --$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 }") );
- }
}
Maasha::Common::error( qq(no --database specified) ) if $script eq "remove_ucsc_tracks" and not $options{ "database" };
}
-sub script_read_psl
-{
- # Martin A. Hansen, August 2007.
-
- # Read psl table from stream or file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $file, $data_in, $num );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) ) {
- Maasha::Biopieces::put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = Maasha::Common::read_open( $file );
-
- while ( $record = Maasha::UCSC::psl_get_entry( $data_in ) )
- {
- Maasha::Biopieces::put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
- }
-
- NUM:
-}
-
-
sub script_read_stockholm
{
# Martin A. Hansen, August 2007.
}
-sub script_read_soft
-{
- # Martin A. Hansen, December 2007.
-
- # Read soft format.
- # http://www.ncbi.nlm.nih.gov/geo/info/soft2.html
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $data_in, $file, $num, $records, $record, $soft_index, $fh, @platforms, $plat_table, @samples, $sample, $old_end, $skip );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) ) {
- Maasha::Biopieces::put_record( $record, $out );
- }
-
- $num = 1;
-
- 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 { $_->{ "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 ]->{ "LINE_BEG" }, $platforms[ -1 ]->{ "LINE_END" } );
-
- @samples = grep { $_->{ "SECTION" } =~ /SAMPLE/ } @{ $soft_index };
-
- $old_end = $platforms[ -1 ]->{ "LINE_END" };
-
- foreach $sample ( @samples )
- {
- $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 } )
- {
- Maasha::Biopieces::put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- $old_end = $sample->{ "LINE_END" };
- }
-
- close $fh;
- }
-
- NUM:
-
- close $data_in if $data_in;
- close $fh if $fh;
-}
-
-
-sub script_read_solexa
-{
- # Martin A. Hansen, March 2008.
-
- # Read Solexa sequence reads from file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $file, $data_in, $entry, $num, @seqs, @scores, $i );
-
- $options->{ "format" } ||= "octal";
- $options->{ "quality" } ||= 20;
-
- while ( $record = Maasha::Biopieces::get_record( $in ) ) {
- Maasha::Biopieces::put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = Maasha::Common::read_open( $file );
-
- if ( $options->{ "format" } eq "octal" )
- {
- while ( $entry = Maasha::Solexa::solexa_get_entry_octal( $data_in ) )
- {
- $record = Maasha::Solexa::solexa2biopiece( $entry, $options->{ "quality" } );
-
- Maasha::Biopieces::put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
- }
- else
- {
- while ( $entry = Maasha::Solexa::solexa_get_entry_decimal( $data_in ) )
- {
- $record = Maasha::Solexa::solexa2biopiece( $entry, $options->{ "quality" } );
-
- Maasha::Biopieces::put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
- }
-
- close $data_in;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
sub script_read_solid
{
# Martin A. Hansen, April 2008.
projects / biopieces.git / blobdiff