use Storable qw( dclone );
use Maasha::Config;
use Maasha::Common;
+use Maasha::Filesys;
use Maasha::Fasta;
use Maasha::Align;
use Maasha::Matrix;
use Maasha::Plot;
use Maasha::Calc;
use Maasha::UCSC;
+use Maasha::UCSC::BED;
+use Maasha::UCSC::Wiggle;
use Maasha::NCBI;
use Maasha::GFF;
use Maasha::TwoBit;
use Maasha::Solid;
+use Maasha::Solexa;
use Maasha::SQL;
use Maasha::Gwiki;
my ( $script, $BP_TMP );
-$script = Maasha::Common::get_scriptname();
-$BP_TMP = Maasha::Common::get_tmpdir();
+$script = Maasha::Common::get_scriptname();
+$BP_TMP = Maasha::Common::get_tmpdir();
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LOG <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my $log_fh = Maasha::Common::append_open( "$ENV{ 'BP_TMP' }/biopieces.log" );
+my $log_global = Maasha::Common::append_open( "$ENV{ 'BP_LOG' }/biopieces.log" );
+my $log_local = Maasha::Common::append_open( "$ENV{ 'HOME' }/.biopieces.log" );
-$log_fh->autoflush( 1 );
+$log_global->autoflush( 1 );
+$log_local->autoflush( 1 );
-&log( $log_fh, $script, \@ARGV );
+&log( $log_global, $script, \@ARGV );
+&log( $log_local, $script, \@ARGV );
-close $log_fh;
+close $log_global;
+close $log_local;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RUN SCRIPT <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my $t0 = gettimeofday();
-
run_script( $script );
-my $t1 = gettimeofday();
-
-print STDERR "Program: $script" . ( " " x ( 25 - length( $script ) ) ) . sprintf( "Run time: %.4f\n", ( $t1 - $t0 ) );
-
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
# Returns nothing.
- my ( $options, $in, $out );
+ my ( $t0, $t1, $options, $in, $out );
+
+ $t0 = gettimeofday();
$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' } );
}
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 "read_ucsc_config" ) { script_read_ucsc_config( $in, $out, $options ) }
+ elsif ( $script eq "assemble_tag_contigs" ) { script_assemble_tag_contigs( $in, $out, $options ) }
elsif ( $script eq "format_genome" ) { script_format_genome( $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 "oligo_freq" ) { script_oligo_freq( $in, $out, $options ) }
elsif ( $script eq "create_weight_matrix" ) { script_create_weight_matrix( $in, $out, $options ) }
elsif ( $script eq "calc_bit_scores" ) { script_calc_bit_scores( $in, $out, $options ) }
+ elsif ( $script eq "calc_fixedstep" ) { script_calc_fixedstep( $in, $out, $options ) }
elsif ( $script eq "reverse_seq" ) { script_reverse_seq( $in, $out, $options ) }
elsif ( $script eq "complement_seq" ) { script_complement_seq( $in, $out, $options ) }
elsif ( $script eq "remove_indels" ) { script_remove_indels( $in, $out, $options ) }
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 ) }
elsif ( $script eq "write_fixedstep" ) { script_write_fixedstep( $in, $out, $options ) }
elsif ( $script eq "write_2bit" ) { script_write_2bit( $in, $out, $options ) }
elsif ( $script eq "write_solid" ) { script_write_solid( $in, $out, $options ) }
+ elsif ( $script eq "write_ucsc_config" ) { script_write_ucsc_config( $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 "remove_mysql_tables" ) { script_remove_mysql_tables( $in, $out, $options ) }
+ elsif ( $script eq "remove_ucsc_tracks" ) { script_remove_ucsc_tracks( $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 ) }
close $in if defined $in;
close $out;
- # unset status - missing
- # write log file - missing
+ $t1 = gettimeofday();
+
+ print STDERR "Program: $script" . ( " " x ( 25 - length( $script ) ) ) . sprintf( "Run time: %.4f\n", ( $t1 - $t0 ) ) if $options->{ 'verbose' };
}
# Returns hash
- my ( %options, @options, $opt, @genomes );
+ my ( %options, @options, $opt, @genomes, $real );
if ( $script eq "print_usage" )
{
{
@options = qw(
data_in|i=s
+ cols|c=s
num|n=s
+ check|C
);
}
elsif ( $script eq "read_fixedstep" )
{
@options = qw(
data_in|i=s
+ samples|s=s
num|n=s
);
}
@options = qw(
data_in|i=s
num|n=s
+ format|f=s
quality|q=s
);
}
password|p=s
);
}
+ elsif ( $script eq "read_ucsc_config" )
+ {
+ @options = qw(
+ data_in|i=s
+ num|n=s
+ );
+ }
+ elsif ( $script eq "assemble_tag_contigs" )
+ {
+ @options = qw(
+ check|C
+ );
+ }
+ elsif ( $script eq "calc_fixedstep" )
+ {
+ @options = qw(
+ check|C
+ );
+ }
elsif ( $script eq "format_genome" )
{
@options = qw(
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(
elsif ( $script eq "write_bed" )
{
@options = qw(
+ cols|c=s
+ check|C
no_stream|x
data_out|o=s
compress|Z
compress|Z
);
}
+ elsif ( $script eq "write_ucsc_config" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ );
+ }
elsif ( $script eq "plot_seqlogo" )
{
@options = qw(
save_keys|K=s
);
}
+ elsif ( $script eq "remove_adaptor" )
+ {
+ @options = qw(
+ adaptor|a=s
+ mismatches|m=s
+ remove|r=s
+ offset|o=s
+ );
+ }
+ elsif ( $script eq "remove_mysql_tables" )
+ {
+ @options = qw(
+ database|d=s
+ tables|t=s
+ keys|k=s
+ user|u=s
+ password|p=s
+ no_stream|x
+ );
+ }
+ elsif ( $script eq "remove_ucsc_tracks" )
+ {
+ @options = qw(
+ database|d=s
+ tracks|t=s
+ keys|k=s
+ config_file|c=s
+ user|u=s
+ password|p=s
+ no_stream|x
+ );
+ }
elsif ( $script eq "rename_keys" )
{
@options = qw(
delimit|d=s
);
}
+ elsif ( $script eq "merge_records" )
+ {
+ @options = qw(
+ keys|k=s
+ merge|m=s
+ );
+ }
elsif ( $script eq "grab" )
{
@options = qw(
group|g=s
priority|p=f
use_score|u
- visibility|v=s
- wiggle|w
+ visibility|V=s
color|c=s
- chunk_size|C=s
+ check|C
);
}
push @options, qw(
stream_in|I=s
stream_out|O=s
- verbose
+ verbose|v
help|?
);
# 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;
}
$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" };
+ $options{ "tables" } = [ split ",", $options{ "tables" } ] if defined $options{ "tables" };
+ $options{ "tracks" } = [ split ",", $options{ "tracks" } ] if defined $options{ "tracks" };
# ---- check arguments ----
map { Maasha::Common::error( qq(Argument to --cols must be a whole numbers - not "$_") ) if $_ !~ /^\d+$/ } @{ $options{ "cols" } } if $options{ "cols" };
-# print STDERR Dumper( \%options );
+ # print STDERR Dumper( \%options );
+
+ $real = "beg|end|word_size|wrap|tile_size|len|prefix_length|mismatches|offset|num|skip|cpus|window_size|step_size";
foreach $opt ( keys %options )
{
{
Maasha::Common::error( qq(Argument to --$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 }") );
}
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 '$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 }") );
+ }
+ elsif ( $opt eq "remove" and $script eq "remove_adaptor" and $options{ $opt } !~ /before|after|skip/ )
{
- Maasha::Common::error( qq(Character '$options{ $opt }' is not allowed in table names) );
+ Maasha::Common::error( qq(Argument to --$opt must be before, after, or skip - not "$options{ $opt }") );
}
}
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" };
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 );
@{ $wiki } = grep { $_->[ 0 ]->{ 'FORMAT' } =~ /paragraph/ } @{ $wiki };
$synopsis = $wiki->[ 0 ]->[ 0 ]->{ 'TEXT' };
+ $synopsis =~ s/!(\w)/$1/g;
printf( "%-30s%s\n", $program, $synopsis );
}
# Returns nothing.
- my ( $record, @files, $file, $entries, $entry, $num );
+ my ( $record, $file, $data_in, $num );
while ( $record = get_record( $in ) ) {
put_record( $record, $out );
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" };
# Returns nothing.
- my ( $file, $record, $entry, $data_in, $num );
+ my ( $cols, $file, $record, $bed_entry, $data_in, $num );
+
+ $cols = $options->{ 'cols' }->[ 0 ];
while ( $record = get_record( $in ) ) {
put_record( $record, $out );
{
$data_in = Maasha::Common::read_open( $file );
- while ( $entry = Maasha::UCSC::bed_get_entry( $data_in ) )
+ while ( $bed_entry = Maasha::UCSC::BED::bed_entry_get( $data_in, $cols, $options->{ 'check' } ) )
{
- put_record( $entry, $out );
+ $record = Maasha::UCSC::BED::bed2biopiece( $bed_entry );
+
+ put_record( $record, $out );
goto NUM if $options->{ "num" } and $num == $options->{ "num" };
{
# Martin A. Hansen, Juli 2008.
- # Read fixedStep wiggle format from stream or file.
+ # Read fixedstep wiggle format from stream or file.
my ( $in, # handle to in stream
$out, # handle to out stream
# Returns nothing.
- my ( $file, $record, $entry, $head, $chr, $chr_beg, $step, $data_in, $num );
+ my ( $file, $record, $entry, $data_in, $num );
while ( $record = get_record( $in ) ) {
put_record( $record, $out );
{
$data_in = Maasha::Common::read_open( $file );
- while ( $entry = Maasha::UCSC::fixedstep_get_entry( $data_in ) )
+ while ( $entry = Maasha::UCSC::Wiggle::fixedstep_entry_get( $data_in ) )
{
- $head = shift @{ $entry };
-
- if ( $head =~ /^chrom=([^ ]+) start=(\d+) step=(\d+)$/ )
- {
- $record->{ "CHR" } = $1;
- $record->{ "CHR_BEG" } = $2;
- $record->{ "STEP" } = $3;
- $record->{ "VALS" } = join ",", @{ $entry };
- }
+ $record = Maasha::UCSC::Wiggle::fixedstep2biopiece( $entry );
put_record( $record, $out );
# 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 );
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 } )
{
$num++;
}
- $old_end = $sample->[ 2 ];
+ $old_end = $sample->{ "LINE_END" };
}
close $fh;
# 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 ) ) {
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;
}
$record = {
+ REC_TYPE => 'SOLID',
SEQ_NAME => $seq_name,
SEQ_CS => $seq_cs,
- SEQ_QUAL => $seq_qual,
+ SEQ_QUAL => join( ";", @scores ),
SEQ_LEN => length $seq_cs,
SEQ => join( "", @seqs ),
SCORE_MEAN => sprintf( "%.2f", Maasha::Calc::mean( \@scores ) ),
}
+sub script_read_ucsc_config
+{
+ # Martin A. Hansen, November 2008.
+
+ # Read track entries from UCSC Genome Browser '.ra' files.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $file, $data_in, $entry, $num );
+
+ while ( $record = get_record( $in ) ) {
+ put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $data_in = Maasha::Common::read_open( $file );
+
+ while ( $record = Maasha::UCSC::ucsc_config_entry_get( $data_in ) )
+ {
+ $record->{ 'REC_TYPE' } = "UCSC Config";
+
+ 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_assemble_tag_contigs
+{
+ # Martin A. Hansen, November 2008.
+
+ # Assemble tags from the stream into
+ # tag contigs.
+
+ # The current implementation is quite
+ # slow because of heavy use of temporary
+ # files.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $bed_file, $tag_file, $fh_in, $fh_out, $cols, $record, $bed_entry, $file_hash, $chr, $strand );
+
+ $bed_file = "$BP_TMP/assemble_tag_contigs.bed";
+ $fh_out = Maasha::Filesys::file_write_open( $bed_file );
+ $cols = 6; # we only need the first 6 BED columns
+
+ while ( $record = get_record( $in ) )
+ {
+ if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record, $cols ) )
+ {
+ $strand = $record->{ 'STRAND' } || '+';
+
+ Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh_out, $cols, $options->{ 'check' } );
+ }
+ }
+
+ close $fh_out;
+
+ $file_hash = Maasha::UCSC::BED::bed_file_split_on_chr( $bed_file, $BP_TMP, $cols );
+
+ unlink $bed_file;
+
+ foreach $chr ( sort keys %{ $file_hash } )
+ {
+ $bed_file = $file_hash->{ $chr };
+ $tag_file = "$bed_file.tc";
+
+ Maasha::Common::run( "bed2tag_contigs", "< $bed_file > $tag_file" );
+
+ $fh_in = Maasha::Filesys::file_read_open( $tag_file );
+
+ while ( $bed_entry = Maasha::UCSC::BED::bed_entry_get( $fh_in, $cols, $options->{ 'check' } ) )
+ {
+ if ( $record = Maasha::UCSC::BED::bed2biopiece( $bed_entry ) ) {
+ put_record( $record, $out );
+ }
+ }
+
+ close $fh_in;
+
+ unlink $bed_file;
+ unlink $tag_file;
+ }
+}
+
+
sub script_format_genome
{
# Martin A. Hansen, Juli 2008.
# 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' };
while ( $record = get_record( $in ) )
{
- if ( $fh_out and $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+ if ( $fh_out and $entry = Maasha::Fasta::biopiece2fasta( $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" } )
{
}
+sub script_calc_fixedstep
+{
+ # Martin A. Hansen, September 2008.
+
+ # Calculates fixedstep entries from data in the stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $bed_file, $fh_in, $fh_out, $cols, $record, $file_hash, $chr, $bed_entry, $fixedstep_file, $fixedstep_entry );
+
+ $bed_file = "$BP_TMP/calc_fixedstep.bed";
+ $fh_out = Maasha::Filesys::file_write_open( $bed_file );
+ $cols = 5; # we only need the first 5 BED columns
+
+ while ( $record = get_record( $in ) )
+ {
+ if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record, $cols ) ) {
+ Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh_out, $cols, $options->{ 'check' } );
+ }
+ }
+
+ close $fh_out;
+
+ $file_hash = Maasha::UCSC::BED::bed_file_split_on_chr( $bed_file, $BP_TMP, $cols );
+
+ unlink $bed_file;
+
+ foreach $chr ( sort keys %{ $file_hash } )
+ {
+ $bed_file = $file_hash->{ $chr };
+ $fixedstep_file = "$bed_file.fixedstep";
+
+ Maasha::Common::run( "bed2fixedstep", "< $bed_file > $fixedstep_file" );
+
+ $fh_in = Maasha::Filesys::file_read_open( $fixedstep_file );
+
+ while ( $fixedstep_entry = Maasha::UCSC::Wiggle::fixedstep_entry_get( $fh_in ) )
+ {
+ if ( $record = Maasha::UCSC::Wiggle::fixedstep2biopiece( $fixedstep_entry ) ) {
+ put_record( $record, $out );
+ }
+ }
+
+ close $fh_in;
+
+ unlink $bed_file;
+ unlink $fixedstep_file;
+ }
+}
+
+
sub script_reverse_seq
{
# Martin A. Hansen, August 2007.
{
$align = Maasha::UCSC::maf_extract( $BP_TMP, $options->{ "genome" }, $maf_track, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $record->{ "STRAND" } );
}
+ elsif ( $record->{ "REC_TYPE" } eq "VMATCH" )
+ {
+ $align = Maasha::UCSC::maf_extract( $BP_TMP, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" } + 1, $record->{ "STRAND" } );
+ }
elsif ( $record->{ "REC_TYPE" } eq "PSL" )
{
$align = Maasha::UCSC::maf_extract( $BP_TMP, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $record->{ "STRAND" } );
$phastcons_file = Maasha::Config::genome_phastcons( $options->{ "genome" } );
$phastcons_index = Maasha::Config::genome_phastcons_index( $options->{ "genome" } );
- $index = Maasha::UCSC::phastcons_index_retrieve( $phastcons_index );
+ $index = Maasha::UCSC::fixedstep_index_retrieve( $phastcons_index );
$fh_phastcons = Maasha::Common::read_open( $phastcons_file );
if ( defined $options->{ "chr" } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) )
$options->{ "end" } = $options->{ "beg" } + $options->{ "len" } - 1;
}
- $scores = Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $options->{ "chr" }, $options->{ "beg" }, $options->{ "end" }, $options->{ "flank" } );
+ $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $options->{ "chr" }, $options->{ "beg" }, $options->{ "end" }, $options->{ "flank" } );
$record->{ "CHR" } = $options->{ "chr" };
$record->{ "CHR_BEG" } = $options->{ "beg" } - $options->{ "flank" };
{
if ( $record->{ "REC_TYPE" } eq "BED" )
{
- $scores = Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "flank" } );
+ $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "flank" } );
}
elsif ( $record->{ "REC_TYPE" } eq "PSL" )
{
- $scores = Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $options->{ "flank" } );
+ $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $options->{ "flank" } );
}
elsif ( $record->{ "REC_TYPE" } eq "BLAST" )
{
- $scores = Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $options->{ "flank" } );
+ $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $options->{ "flank" } );
}
$record->{ "PHASTCONS" } = join ",", @{ $scores } if @{ $scores };
$i++;
}
-
-# put_record( $record, $out );
}
close $fh_out;
# Returns nothing.
- my ( $fh, $seq_type, $path, $record );
+ my ( $fh, $seq_type, $path, $record, $entry );
$path = $options->{ "database" };
{
put_record( $record, $out ) if not $options->{ "no_stream" };
- if ( $record->{ "SEQ" } and $record->{ "SEQ_NAME" } )
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $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 );
}
}
# 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";
- $fh_out = Maasha::Common::write_open( $tmp_in );
+ $fh_out = Maasha::Filesys::file_write_open( $tmp_in );
while ( $record = get_record( $in ) )
{
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $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 );
}
}
- 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;
- $fh_out = Maasha::Common::read_open( $tmp_out );
+ $fh_out = Maasha::Filesys::file_read_open( $tmp_out );
undef $record;
# 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";
while ( $record = get_record( $in ) )
{
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $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 );
}
-sub script_match_seq
+sub script_soap_seq
{
- # Martin A. Hansen, August 2007.
+ # Martin A. Hansen, July 2008.
- # BLATs sequences in stream against a given genome.
+ # soap sequences in stream against a given file or genome.
my ( $in, # handle to in stream
$out, # handle to out stream
# Returns nothing.
- my ( $record, @entries, $results );
-
- $options->{ "word_size" } ||= 20;
- $options->{ "direction" } ||= "both";
+ my ( $genome, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $line, @fields, $entry, $count, $args );
- while ( $record = get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
- push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
- }
+ $options->{ "seed_size" } ||= 10;
+ $options->{ "mismatches" } ||= 2;
+ $options->{ "gap_size" } ||= 0;
+ $options->{ "cpus" } ||= 1;
- put_record( $record, $out );
+ if ( $options->{ "genome" } ) {
+ $options->{ "in_file" } = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna";
}
- if ( @entries == 1 )
- {
- $results = Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 0 ] ], $options, $BP_TMP );
+ $tmp_in = "$BP_TMP/soap_query.seq";
+ $tmp_out = "$BP_TMP/soap.result";
- map { put_record( $_, $out ) } @{ $results };
+ $fh_out = Maasha::Common::write_open( $tmp_in );
+
+ $count = 0;
+
+ while ( $record = get_record( $in ) )
+ {
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $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.
+
+ # BLATs sequences in stream against a given genome.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, @entries, $results );
+
+ $options->{ "word_size" } ||= 20;
+ $options->{ "direction" } ||= "both";
+
+ while ( $record = get_record( $in ) )
+ {
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
+ push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+ }
+
+ put_record( $record, $out );
+ }
+
+ if ( @entries == 1 )
+ {
+ $results = Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 0 ] ], $options, $BP_TMP );
+
+ map { put_record( $_, $out ) } @{ $results };
}
elsif ( @entries == 2 )
{
# Returns nothing.
- my ( $record, $file_tmp, $fh_tmp, $type );
+ my ( $record, $file_tmp, $fh_tmp, $type, $entry );
if ( $options->{ "index_name" } )
{
while ( $record = get_record( $in ) )
{
- if ( $options->{ "index_name" } and $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+ if ( $options->{ "index_name" } and $entry = Maasha::Fasta::biopiece2fasta( $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" };
# 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 = Maasha::Fasta::biopiece2fasta( $record ) ) {
+ Maasha::Fasta::put_entry( $entry, $fh, $options->{ "wrap" } );
}
put_record( $record, $out ) if not $options->{ "no_stream" };
# Returns nothing.
- my ( $fh, $record, $new_record );
+ my ( $cols, $fh, $record, $bed_entry, $new_record );
- $fh = write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+ $cols = $options->{ 'cols' }->[ 0 ];
+
+ $fh = write_stream( $options->{ 'data_out' }, $options->{ 'compress' } );
while ( $record = get_record( $in ) )
{
- if ( $record->{ "REC_TYPE" } eq "BED" ) # ---- Hits from BED ----
- {
- Maasha::UCSC::bed_put_entry( $record, $fh, $record->{ "BED_COLS" } );
- }
- elsif ( $record->{ "REC_TYPE" } eq "PSL" and $record->{ "S_ID" } =~ /^chr/i ) # ---- Hits from BLAT (PSL) ----
- {
- $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->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "CHR" } ) # ---- Hits from patscan_seq ----
- {
- Maasha::UCSC::bed_put_entry( $record, $fh, 6 );
- }
- elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/i ) # ---- Hits from BLAST ----
- {
- $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; # or use E_VAL somehow
- $new_record->{ "STRAND" } = $record->{ "STRAND" };
-
- Maasha::UCSC::bed_put_entry( $new_record, $fh, 6 );
- }
- elsif ( $record->{ "REC_TYPE" } eq "VMATCH" 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; # or use E_VAL somehow
- $new_record->{ "STRAND" } = $record->{ "STRAND" };
+ $record = Maasha::UCSC::psl2record( $record ) if $record->{ 'tBaseInsert' }; # Dirty addition to allow Affy data from MySQL to be dumped
- 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 );
+ if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record, $cols ) ) {
+ Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh, $cols, $options->{ 'check' } );
}
- put_record( $record, $out ) if not $options->{ "no_stream" };
+ put_record( $record, $out ) if not $options->{ 'no_stream' };
}
close $fh;
# Returns nothing.
- my ( $fh, $record, $vals );
+ my ( $fh, $record, $entry );
$fh = write_stream( $options->{ "data_out" }, $options->{ "compress" } );
while ( $record = get_record( $in ) )
{
- if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "STEP" } and $record->{ "VALS" } )
- {
- print $fh "fixedStep chrom=$record->{ 'CHR' } start=$record->{ 'CHR_BEG' } step=$record->{ 'STEP' }\n";
-
- $vals = $record->{ 'VALS' };
-
- $vals =~ tr/,/\n/;
-
- print $fh "$vals\n";
+ if ( $entry = Maasha::UCSC::Wiggle::biopiece2fixedstep( $record ) ) {
+ Maasha::UCSC::Wiggle::fixedstep_entry_put( $entry, $fh );
}
put_record( $record, $out ) if not $options->{ "no_stream" };
# 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" };
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 = Maasha::Fasta::biopiece2fasta( $record ) ) {
+ Maasha::Fasta::put_entry( $entry, $fh_tmp );
}
put_record( $record, $out ) if not $options->{ "no_stream" };
# 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 = Maasha::Fasta::biopiece2fasta( $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" };
}
+sub script_write_ucsc_config
+{
+ # Martin A. Hansen, November 2008.
+
+ # Write UCSC Genome Broser configuration (.ra file type) from
+ # records in the stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $fh );
+
+ $fh = write_stream( $options->{ "data_out" } );
+
+ while ( $record = get_record( $in ) )
+ {
+ Maasha::UCSC::ucsc_config_entry_put( $record, $fh ) if $record->{ "REC_TYPE" } eq "UCSC Config";
+
+ put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ close $fh;
+}
+
+
sub script_plot_seqlogo
{
# Martin A. Hansen, August 2007.
$phastcons_file = Maasha::Config::genome_phastcons( $options->{ "genome" } );
$phastcons_index = Maasha::Config::genome_phastcons_index( $options->{ "genome" } );
- $index = Maasha::UCSC::phastcons_index_retrieve( $phastcons_index );
+ $index = Maasha::UCSC::fixedstep_index_retrieve( $phastcons_index );
$fh_phastcons = Maasha::Common::read_open( $phastcons_file );
while ( $record = get_record( $in ) )
{
if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
{
- $scores = Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "flank" } );
+ $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "CHR" },
+ $record->{ "CHR_BEG" },
+ $record->{ "CHR_END" },
+ $options->{ "flank" } );
push @{ $AoA }, [ @{ $scores } ];
}
}
+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 );
+
+ $options->{ "remove" } ||= "after";
+
+ $max_mismatch = $options->{ "mismatches" } || 0;
+ $offset = $options->{ "offset" };
+
+ if ( not defined $offset ) {
+ $offset = 0;
+ } else {
+ $offset--;
+ }
+
+ $adaptor = uc $options->{ "adaptor" };
+ $adaptor_len = length $adaptor;
+
+ while ( $record = get_record( $in ) )
+ {
+ if ( $record->{ "SEQ" } )
+ {
+ $seq = uc $record->{ "SEQ" };
+ $seq_len = length $seq;
+
+ $pos = Maasha::Common::index_m( $seq, $adaptor, $seq_len, $adaptor_len, $offset, $max_mismatch );
+
+ $record->{ "ADAPTOR_POS" } = $pos;
+
+ if ( $pos >= 0 and $options->{ "remove" } ne "skip" )
+ {
+ if ( $options->{ "remove" } eq "after" )
+ {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, 0, $pos;
+ $record->{ "SEQ_LEN" } = $pos;
+ }
+ else
+ {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $pos + $adaptor_len;
+ $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
+ }
+ }
+
+ put_record( $record, $out );
+ }
+ else
+ {
+ put_record( $record, $out );
+ }
+ }
+}
+
+
+sub script_remove_mysql_tables
+{
+ # Martin A. Hansen, November 2008.
+
+ # Remove MySQL tables from values in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, %table_hash, $dbh, $table );
+
+ $options->{ "user" } ||= Maasha::UCSC::ucsc_get_user();
+ $options->{ "password" } ||= Maasha::UCSC::ucsc_get_password();
+
+ map { $table_hash{ $_ } = 1 } @{ $options->{ 'tables' } };
+
+ while ( $record = get_record( $in ) )
+ {
+ map { $table_hash{ $record->{ $_ } } = 1 } @{ $options->{ 'keys' } };
+
+ put_record( $record, $out ) if not $options->{ 'no_stream' };
+ }
+
+ $dbh = Maasha::SQL::connect( $options->{ "database" }, $options->{ "user" }, $options->{ "password" } );
+
+ foreach $table ( sort keys %table_hash )
+ {
+ if ( Maasha::SQL::table_exists( $dbh, $table ) )
+ {
+ print STDERR qq(Removing table "$table" from database "$options->{ 'database' }" ... ) if $options->{ 'verbose' };
+ Maasha::SQL::delete_table( $dbh, $table );
+ print STDERR "done.\n" if $options->{ 'verbose' };
+ }
+ else
+ {
+ print STDERR qq(WARNING: table "$table" not found in database "$options->{ 'database' }\n");
+ }
+ }
+
+ Maasha::SQL::disconnect( $dbh );
+}
+
+
+sub script_remove_ucsc_tracks
+{
+ # Martin A. Hansen, November 2008.
+
+ # Remove track from MySQL tables and config file.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, %track_hash, $fh_in, $fh_out, $track, @tracks, @new_tracks, $dbh );
+
+ $options->{ 'user' } ||= Maasha::UCSC::ucsc_get_user();
+ $options->{ 'password' } ||= Maasha::UCSC::ucsc_get_password();
+ $options->{ 'config_file' } ||= "$ENV{ 'HOME' }/ucsc/my_tracks.ra";
+
+ map { $track_hash{ $_ } = 1 } @{ $options->{ 'tracks' } };
+
+ while ( $record = get_record( $in ) )
+ {
+ map { $track_hash{ $record->{ $_ } } = 1 } @{ $options->{ 'keys' } };
+
+ put_record( $record, $out ) if not $options->{ 'no_stream' };
+ }
+
+ # ---- locate track in config file ----
+
+ $fh_in = Maasha::Common::read_open( $options->{ 'config_file' } );
+
+ while ( $track = Maasha::UCSC::ucsc_config_entry_get( $fh_in ) ) {
+ push @tracks, $track;
+ }
+
+ close $fh_in;
+
+ map { push @new_tracks, $_ if not exists $track_hash{ $_->{ 'track' } } } @tracks;
+
+ print STDERR qq(WARNING: track not found in config file: "$options->{ 'config_file' }"\n) if scalar @tracks == scalar @new_tracks;
+
+ rename "$options->{ 'config_file' }", "$options->{ 'config_file' }~";
+
+ $fh_out = Maasha::Common::write_open( $options->{ 'config_file' } );
+
+ map { Maasha::UCSC::ucsc_config_entry_put( $_, $fh_out ) } @new_tracks;
+
+ close $fh_out;
+
+ # ---- locate track in database ----
+
+ $dbh = Maasha::SQL::connect( $options->{ "database" }, $options->{ "user" }, $options->{ "password" } );
+
+ foreach $track ( sort keys %track_hash )
+ {
+ if ( Maasha::SQL::table_exists( $dbh, $track ) )
+ {
+ print STDERR qq(Removing table "$track" from database "$options->{ 'database' }" ... ) if $options->{ 'verbose' };
+ Maasha::SQL::delete_table( $dbh, $track );
+ print STDERR "done.\n" if $options->{ 'verbose' };
+ }
+ else
+ {
+ print STDERR qq(WARNING: table "$track" not found in database "$options->{ 'database' }\n");
+ }
+ }
+
+ Maasha::SQL::disconnect( $dbh );
+
+ Maasha::Common::run( "ucscMakeTracks.pl", "-b > /dev/null 2>&1" );
+}
+
+
sub script_rename_keys
{
# Martin A. Hansen, August 2007.
}
-sub script_grab
+sub script_merge_records
{
- # Martin A. Hansen, August 2007.
+ # Martin A. Hansen, July 2008.
- # Grab for records in stream.
+ # Merges records in the stream based on identical values of two given keys.
my ( $in, # handle to in stream
$out, # handle to out stream
# Returns nothing.
- my ( $patterns, $pattern, $record, $key, $pos, $op, $val, %lookup_hash );
+ 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";
- if ( $options->{ "patterns" } )
+ $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 ) )
{
- $patterns = [ split ",", $options->{ "patterns" } ];
+ 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++;
+ }
}
- elsif ( -f $options->{ "patterns_in" } )
+
+ close $fh1;
+ close $fh2;
+
+ if ( $num )
{
- $patterns = Maasha::Patscan::read_patterns( $options->{ "patterns_in" } );
+ 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;
}
- elsif ( -f $options->{ "exact_in" } )
+ else
{
- $patterns = Maasha::Patscan::read_patterns( $options->{ "exact_in" } );
+ 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;
+ }
- map { $lookup_hash{ $_ } = 1 } @{ $patterns };
+ $fh1 = Maasha::Common::read_open( $file1 );
+ $fh2 = Maasha::Common::read_open( $file2 );
- undef $patterns;
- }
+ @vals1 = Maasha::Common::get_fields( $fh1 );
+ @vals2 = Maasha::Common::get_fields( $fh2 );
- if ( $options->{ "eval" } )
+ while ( $num1 > 0 and $num2 > 0 )
{
- if ( $options->{ "eval" } =~ /^([^><=! ]+)\s*(>=|<=|>|<|=|!=|eq|ne)\s*(.+)$/ )
- {
- $key = $1;
- $op = $2;
- $val = $3;
+ undef $record;
+
+ if ( $num ) {
+ $cmp = $vals1[ 0 ] <=> $vals2[ 0 ];
+ } else {
+ $cmp = $vals1[ 0 ] cmp $vals2[ 0 ];
}
- }
- while ( $record = get_record( $in ) )
- {
- $pos = -1;
-
- if ( %lookup_hash )
+ if ( $cmp < 0 )
{
- if ( $options->{ "keys" } )
+ if ( $merge =~ /^(AorB|AnotB)$/ )
{
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( exists $lookup_hash{ $record->{ $key } } )
- {
- $pos = 1;
- goto FOUND;
- }
+ for ( $i = 0; $i < @keys1; $i++ ) {
+ $record->{ $keys1[ $i ] } = $vals1[ $i ];
}
- }
- else
- {
- foreach $key ( keys %{ $record } )
- {
- if ( not $options->{ "vals_only" } )
- {
- if ( exists $lookup_hash{ $key } )
- {
- $pos = 1;
- goto FOUND;
- }
- }
- if ( not $options->{ "keys_only" } )
- {
- if ( exists $lookup_hash{ $record->{ $key } } )
- {
- $pos = 1;
- goto FOUND;
- }
- }
- }
+ put_record( $record, $out );
}
+
+ @vals1 = Maasha::Common::get_fields( $fh1 );
+ $num1--;
}
- elsif ( $patterns )
+ elsif ( $cmp > 0 )
{
- foreach $pattern ( @{ $patterns } )
+ if ( $merge =~ /^(BorA|BnotA)$/ )
{
- if ( $options->{ "keys" } )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- $pos = index $record->{ $key }, $pattern;
-
- goto FOUND if $pos >= 0;
- }
+ for ( $i = 0; $i < @keys2; $i++ ) {
+ $record->{ $keys2[ $i ] } = $vals2[ $i ];
}
- else
- {
- foreach $key ( keys %{ $record } )
- {
- if ( not $options->{ "vals_only" } )
- {
- $pos = index $key, $pattern;
- goto FOUND if $pos >= 0;
- }
-
- if ( not $options->{ "keys_only" } )
- {
- $pos = index $record->{ $key }, $pattern;
-
- goto FOUND if $pos >= 0;
- }
- }
- }
+ put_record( $record, $out );
}
+
+ @vals2 = Maasha::Common::get_fields( $fh2 );
+ $num2--;
}
- elsif ( $options->{ "regex" } )
+ else
{
- if ( $options->{ "keys" } )
+ if ( $merge =~ /^(AandB|AorB|BorA)$/ )
{
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( $options->{ "case_insensitive" } ) {
- $pos = 1 if $record->{ $key } =~ /$options->{'regex'}/i;
- } else {
- $pos = 1 if $record->{ $key } =~ /$options->{'regex'}/;
- }
+ for ( $i = 0; $i < @keys1; $i++ ) {
+ $record->{ $keys1[ $i ] } = $vals1[ $i ];
+ }
- goto FOUND if $pos >= 0;
+ for ( $i = 1; $i < @keys2; $i++ ) {
+ $record->{ $keys2[ $i ] } = $vals2[ $i ];
}
+
+ put_record( $record, $out );
}
- else
- {
- foreach $key ( keys %{ $record } )
- {
- if ( not $options->{ "vals_only" } )
- {
- if ( $options->{ "case_insensitive" } ) {
- $pos = 1 if $key =~ /$options->{'regex'}/i;
- } else {
- $pos = 1 if $key =~ /$options->{'regex'}/;
- }
- goto FOUND if $pos >= 0;
- }
+ @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.
+
+ # Grab for records in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
- if ( not $options->{ "keys_only" } )
- {
- if ( $options->{ "case_insensitive" } ) {
- $pos = 1 if $record->{ $key } =~ /$options->{'regex'}/i;
- } else {
- $pos = 1 if $record->{ $key } =~ /$options->{'regex'}/;
- }
+ my ( $keys, $vals_only, $keys_only, $invert, $patterns, $pattern, $regex, $record, $key, $op, $val, %lookup_hash, $found );
- goto FOUND if $pos >= 0;
- }
- }
- }
+ $keys = $options->{ 'keys' };
+ $vals_only = $options->{ 'vals_only' };
+ $keys_only = $options->{ 'keys_only' };
+ $invert = $options->{ 'invert' };
+
+ if ( $options->{ 'patterns' } )
+ {
+ $patterns = [ split ",", $options->{ 'patterns' } ];
+ }
+ elsif ( -f $options->{ 'patterns_in' } )
+ {
+ $patterns = Maasha::Patscan::read_patterns( $options->{ 'patterns_in' } );
+ }
+ elsif ( $options->{ 'regex' } )
+ {
+ if ( $options->{ 'case_insensitive' } ) {
+ $regex = qr/$options->{ 'regex' }/i;
+ } else {
+ $regex = qr/$options->{ 'regex' }/;
}
- elsif ( $options->{ "eval" } )
+ }
+ elsif ( -f $options->{ 'exact_in' } )
+ {
+ $patterns = Maasha::Patscan::read_patterns( $options->{ 'exact_in' } );
+
+ map { $lookup_hash{ $_ } = 1 } @{ $patterns };
+
+ undef $patterns;
+ }
+ elsif ( $options->{ 'eval' } )
+ {
+ if ( $options->{ 'eval' } =~ /^([^><=! ]+)\s*(>=|<=|>|<|=|!=|eq|ne)\s*(.+)$/ )
{
- if ( defined $record->{ $key } )
- {
- if ( $op eq "<" and $record->{ $key } < $val ) {
- $pos = 1 and goto FOUND;
- } elsif ( $op eq ">" and $record->{ $key } > $val ) {
- $pos = 1 and goto FOUND;
- } elsif ( $op eq ">=" and $record->{ $key } >= $val ) {
- $pos = 1 and goto FOUND;
- } elsif ( $op eq "<=" and $record->{ $key } <= $val ) {
- $pos = 1 and goto FOUND;
- } elsif ( $op eq "=" and $record->{ $key } == $val ) {
- $pos = 1 and goto FOUND;
- } elsif ( $op eq "!=" and $record->{ $key } != $val ) {
- $pos = 1 and goto FOUND;
- } elsif ( $op eq "eq" and $record->{ $key } eq $val ) {
- $pos = 1 and goto FOUND;
- } elsif ( $op eq "ne" and $record->{ $key } ne $val ) {
- $pos = 1 and goto FOUND;
- }
- }
+ $key = $1;
+ $op = $2;
+ $val = $3;
}
+ }
+
+ while ( $record = get_record( $in ) )
+ {
+ $found = 0;
- FOUND:
+ if ( %lookup_hash ) {
+ $found = grab_lookup( \%lookup_hash, $record, $keys, $vals_only, $keys_only );
+ } elsif ( $patterns ) {
+ $found = grab_patterns( $patterns, $record, $keys, $vals_only, $keys_only );
+ } elsif ( $regex ) {
+ $found = grab_regex( $regex, $record, $keys, $vals_only, $keys_only );
+ } elsif ( $op ) {
+ $found = grab_eval( $key, $op, $val, $record );
+ }
- if ( $pos >= 0 and not $options->{ "invert" } ) {
+ if ( $found and not $invert ) {
put_record( $record, $out );
- } elsif ( $pos < 0 and $options->{ "invert" } ) {
+ } elsif ( not $found and $invert ) {
put_record( $record, $out );
}
}
# Returns nothing.
- my ( $record, $eval_key, $eval_val, $check, @keys );
+ my ( $record, $eval_key, @keys, $eval_val );
while ( $record = get_record( $in ) )
{
if ( $options->{ "eval" } )
{
- if ( $options->{ "eval" } =~ /^(.+)\s*=\s*(.+)$/ )
+ if ( $options->{ "eval" } =~ /^(\S+)\s*=\s*(.+)$/ )
{
$eval_key = $1;
$eval_val = $2;
- }
- if ( not $check )
- {
- @keys = split /\W+/, $eval_val;
- @keys = grep { ! /^\d+$/ } @keys;
+ if ( not @keys )
+ {
+ @keys = split /\s+|\+|-|\*|\/|\*\*/, $eval_val;
- $check = 1;
- }
+ @keys = grep { exists $record->{ $_ } } @keys;
+ }
- map { $eval_val =~ s/$_/$record->{ $_ }/g } @keys;
+ map { $eval_val =~ s/\Q$_\E/$record->{ $_ }/g } @keys;
- $record->{ $eval_key } = eval "$eval_val" or Maasha::Common::error( "eval failed -> $@" );
+ $record->{ $eval_key } = eval "$eval_val";
+ Maasha::Common::error( qq(eval "$eval_key = $eval_val" failed -> $@) ) if $@;
+ }
+ else
+ {
+ Maasha::Common::error( qq(Bad compute expression: "$options->{ 'eval' }"\n) );
+ }
}
put_record( $record, $out );
}
}
- $result = { "count_records" => $count };
+ $result = { "RECORDS_COUNT" => $count };
$fh = write_stream( $options->{ "data_out" } );
$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 );
while ( $record = get_record( $in ) )
{
- $data_hash{ $record->{ $options->{ "key" } } }++ if $record->{ $options->{ "key" } };
+ $data_hash{ $record->{ $options->{ "key" } } }++ if defined $record->{ $options->{ "key" } };
put_record( $record, $out ) if not $options->{ "no_stream" };
}
while ( $record = get_record( $in ) )
{
- $data_hash{ $record->{ $options->{ "key" } } }++ if $record->{ $options->{ "key" } };
+ $data_hash{ $record->{ $options->{ "key" } } }++ if defined $record->{ $options->{ "key" } };
put_record( $record, $out ) if not $options->{ "no_stream" };
}
# 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
# 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 );
+ my ( $record, $file, $wib_file, $wig_file, $wib_dir, $fh_out, $i, $first, $format, $type, $columns, $append, $entry );
$options->{ "short_label" } ||= $options->{ 'table' };
$options->{ "long_label" } ||= $options->{ 'table' };
$options->{ "color" } ||= join( ",", int( rand( 255 ) ), int( rand( 255 ) ), int( rand( 255 ) ) );
$options->{ "chunk_size" } ||= 10_000_000_000; # Due to 32-bit UCSC compilation really large tables cannot be loaded in one go.
- $file = "$BP_TMP/ucsc_upload.tmp";
-
+ $file = "$BP_TMP/ucsc_upload.tmp";
$append = 0;
+ $first = 1;
+ $i = 0;
- $first = 1;
-
- $i = 0;
+ $fh_out = Maasha::Common::write_open( $file );
- if ( $options->{ 'wiggle' } )
+ while ( $record = get_record( $in ) )
{
- $options->{ "visibility" } = "full";
+ put_record( $record, $out ) if not $options->{ "no_stream" };
- while ( $record = get_record( $in ) )
+ if ( $record->{ "REC_TYPE" } eq "fixed_step" )
{
- put_record( $record, $out ) if not $options->{ "no_stream" };
-
- $record->{ "CHR" } = $record->{ "S_ID" } if not defined $record->{ "CHR" };
- $record->{ "CHR_BEG" } = $record->{ "S_BEG" } if not defined $record->{ "CHR_BEG" };
- $record->{ "CHR_END" } = $record->{ "S_END" } if not defined $record->{ "CHR_END" };
+ $format = "WIGGLE";
- $fh_hash{ $record->{ "CHR" } } = Maasha::Common::write_open( "$BP_TMP/$record->{ 'CHR' }" ) if not exists $fh_hash{ $record->{ "CHR" } };
+ if ( $entry = Maasha::UCSC::Wiggle::biopiece2fixedstep( $record ) ) {
+ Maasha::UCSC::Wiggle::fixedstep_entry_put( $entry, $fh_out );
+ }
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "PSL" )
+ {
+ $format = "PSL";
- $fh_out = $fh_hash{ $record->{ "CHR" } };
+ Maasha::UCSC::psl_put_header( $fh_out ) if $first;
+ Maasha::UCSC::psl_put_entry( $record, $fh_out );
- Maasha::UCSC::bed_put_entry( $record, $fh_out, 5 );
+ $first = 0;
}
-
- map { close $_ } keys %fh_hash;
-
- $fh_out = Maasha::Common::write_open( $file );
-
- foreach $chr ( sort keys %fh_hash )
+ elsif ( $record->{ "REC_TYPE" } eq "BED" and $record->{ "SEC_STRUCT" } )
{
- Maasha::Common::run( "bedSort", "$BP_TMP/$chr $BP_TMP/$chr" );
-
- $fh_in = Maasha::Common::read_open( "$BP_TMP/$chr" );
-
- undef $block;
-
- while ( $entry = Maasha::UCSC::bed_get_entry( $fh_in, 5 ) )
- {
- $chr = $entry->{ 'CHR' };
- $beg = $entry->{ 'CHR_BEG' };
- $end = $entry->{ 'CHR_END' };
- $q_id = $entry->{ 'Q_ID' };
-
- if ( $q_id =~ /_(\d+)$/ ) {
- $clones = $1;
- } else {
- $clones = 1;
- }
-
- if ( $block )
- {
- if ( $beg > $max )
- {
- Maasha::UCSC::fixedstep_put_entry( $chr, $beg_block, $block, $fh_out );
- undef $block;
- }
- else
- {
- for ( $i = $beg - $beg_block; $i < ( $beg - $beg_block ) + ( $end - $beg ); $i++ ) {
- $block->[ $i ] += $clones;
- }
+ # chrom chromStart chromEnd name score strand size secStr conf
- $max = Maasha::Calc::max( $max, $end );
- }
- }
+ $format = "BED_SS";
- if ( not $block )
- {
- $beg_block = $beg;
- $max = $end;
+ print $fh_out join ( "\t",
+ $record->{ "CHR" },
+ $record->{ "CHR_BEG" },
+ $record->{ "CHR_END" } + 1,
+ $record->{ "Q_ID" },
+ $record->{ "SCORE" },
+ $record->{ "STRAND" },
+ $record->{ "SIZE" },
+ $record->{ "SEC_STRUCT" },
+ $record->{ "CONF" },
+ ), "\n";
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "BED" )
+ {
+ $format = "BED";
+ $columns = $record->{ "BED_COLS" };
- for ( $i = 0; $i < ( $end - $beg ); $i++ ) {
- $block->[ $i ] += $clones;
- }
- }
+ if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
+ Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
}
-
- close $fh_in;
-
- Maasha::UCSC::fixedstep_put_entry( $chr, $beg_block, $block, $fh_out );
-
- unlink "$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
- {
- $fh_out = Maasha::Common::write_open( $file );
-
- while ( $record = get_record( $in ) )
+ elsif ( $record->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "CHR" } )
{
- put_record( $record, $out ) if not $options->{ "no_stream" };
-
- if ( $record->{ "REC_TYPE" } eq "PSL" )
- {
- Maasha::UCSC::psl_put_header( $fh_out ) if $first;
- Maasha::UCSC::psl_put_entry( $record, $fh_out );
-
- $first = 0;
+ $format = "BED";
+ $columns = 6;
- $format = "PSL" if not $format;
- }
- elsif ( $record->{ "REC_TYPE" } eq "BED" and $record->{ "SEC_STRUCT" } )
- {
- # chrom chromStart chromEnd name score strand size secStr conf
-
- print $fh_out join ( "\t",
- $record->{ "CHR" },
- $record->{ "CHR_BEG" },
- $record->{ "CHR_END" } + 1,
- $record->{ "Q_ID" },
- $record->{ "SCORE" },
- $record->{ "STRAND" },
- $record->{ "SIZE" },
- $record->{ "SEC_STRUCT" },
- $record->{ "CONF" },
- ), "\n";
-
- $format = "BED_SS" if not $format;
+ if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
+ Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
}
- elsif ( $record->{ "REC_TYPE" } eq "BED" )
- {
- Maasha::UCSC::bed_put_entry( $record, $fh_out, $record->{ "BED_COLS" } );
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/ )
+ {
+ $format = "BED";
+ $columns = 6;
- $format = "BED" if not $format;
- $columns = $record->{ "BED_COLS" } if not $columns;
- }
- elsif ( $record->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "CHR" } )
- {
- Maasha::UCSC::bed_put_entry( $record, $fh_out, 6 );
+ $record->{ "SCORE" } = $record->{ "BIT_SCORE" } * 1000;
- $format = "BED" if not $format;
- $columns = 6 if not $columns;
+ if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
+ Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
}
- elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/ )
- {
- $record->{ "CHR" } = $record->{ "S_ID" };
- $record->{ "CHR_BEG" } = $record->{ "S_BEG" };
- $record->{ "CHR_END" } = $record->{ "S_END" };
- $record->{ "SCORE" } = $record->{ "BIT_SCORE" } * 1000;
-
- $format = "BED" if not $format;
- $columns = 6 if not $columns;
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and $record->{ "S_ID" } =~ /^chr/i )
+ {
+ $format = "BED";
+ $columns = 6;
- Maasha::UCSC::bed_put_entry( $record, $fh_out );
+ if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
+ Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
}
- elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and $record->{ "S_ID" } =~ /^chr/i )
- {
- $record->{ "CHR" } = $record->{ "S_ID" };
- $record->{ "CHR_BEG" } = $record->{ "S_BEG" };
- $record->{ "CHR_END" } = $record->{ "S_END" };
- $record->{ "SCORE" } = $record->{ "SCORE" } || 999;
- $record->{ "SCORE" } = int( $record->{ "SCORE" } );
+ }
- $format = "BED" if not $format;
- $columns = 6 if not $columns;
+ if ( $i == $options->{ "chunk_size" } )
+ {
+ close $fh_out;
- Maasha::UCSC::bed_put_entry( $record, $fh_out, 6 );
+ if ( $format eq "BED" ) {
+ Maasha::UCSC::bed_upload_to_ucsc( $BP_TMP, $file, $options, $append );
+ } elsif ( $format eq "PSL" ) {
+ Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append );
}
- if ( $i == $options->{ "chunk_size" } )
- {
- close $fh_out;
-
- if ( $format eq "BED" ) {
- Maasha::UCSC::bed_upload_to_ucsc( $BP_TMP, $file, $options, $append );
- } elsif ( $format eq "PSL" ) {
- Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append );
- }
-
- unlink $file;
+ unlink $file;
- $first = 1;
+ $first = 1;
- $append = 1;
+ $append = 1;
- $fh_out = Maasha::Common::write_open( $file );
- }
-
- $i++;
+ $fh_out = Maasha::Common::write_open( $file );
}
+
+ $i++;
}
close $fh_out;
}
elsif ( $format eq "BED_SS" )
{
- $options->{ "sec_struct" } = 1;
-
- $type = "sec_struct";
+ $type = "type bed 6 +";
Maasha::UCSC::bed_upload_to_ucsc( $BP_TMP, $file, $options, $append );
}
}
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 );
unlink $file;
- Maasha::UCSC::update_my_tracks( $options, $type );
+ Maasha::UCSC::ucsc_update_config( $options, $type );
}
}
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+sub grab_lookup
+{
+ # Martin A. Hansen, November 2009.
+
+ # Uses keys from a lookup hash to search records. Optionally, a list of
+ # keys can be given so the lookup is limited to these, also, flags
+ # can be given to limit lookup to keys or vals only. Returns 1 if lookup
+ # succeeded, else 0.
+
+ my ( $lookup_hash, # hashref with patterns
+ $record, # hashref
+ $keys, # list of keys - OPTIONAL
+ $vals_only, # only vals flag - OPTIONAL
+ $keys_only, # only keys flag - OPTIONAL
+ ) = @_;
+
+ # Returns boolean.
+
+ if ( $keys )
+ {
+ map { return 1 if exists $lookup_hash->{ $record->{ $_ } } } @{ $keys };
+ }
+ else
+ {
+ if ( not $vals_only ) {
+ map { return 1 if exists $lookup_hash->{ $_ } } keys %{ $record };
+ }
+
+ if ( not $keys_only ) {
+ map { return 1 if exists $lookup_hash->{ $record->{ $_ } } } keys %{ $record };
+ }
+ }
+
+ return 0;
+}
+
+
+sub grab_patterns
+{
+ # Martin A. Hansen, November 2009.
+
+ # Uses patterns to match records containing the pattern as a substring.
+ # Returns 1 if the record is matched, else 0.
+
+ my ( $patterns, # list of patterns
+ $record, # hashref
+ $keys, # list of keys - OPTIONAL
+ $vals_only, # only vals flag - OPTIONAL
+ $keys_only, # only keys flag - OPTIONAL
+ ) = @_;
+
+ # Returns boolean.
+
+ my ( $pattern );
+
+ foreach $pattern ( @{ $patterns } )
+ {
+ if ( $keys )
+ {
+ map { return 1 if index( $record->{ $_ }, $pattern ) >= 0 } @{ $keys };
+ }
+ else
+ {
+ if ( not $vals_only ) {
+ map { return 1 if index( $_, $pattern ) >= 0 } keys %{ $record };
+ }
+
+ if ( not $keys_only ) {
+ map { return 1 if index( $record->{ $_ }, $pattern ) >= 0 } keys %{ $record };
+ }
+ }
+ }
+
+ return 0;
+}
+
+
+sub grab_regex
+{
+ # Martin A. Hansen, November 2009.
+
+ # Uses regex to match records.
+ # Returns 1 if the record is matched, else 0.
+
+ my ( $regex, # regex to match
+ $record, # hashref
+ $keys, # list of keys - OPTIONAL
+ $vals_only, # only vals flag - OPTIONAL
+ $keys_only, # only keys flag - OPTIONAL
+ ) = @_;
+
+ # Returns boolean.
+
+ if ( $keys )
+ {
+ map { return 1 if $record->{ $_ } =~ /$regex/ } @{ $keys };
+ }
+ else
+ {
+ if ( not $vals_only ) {
+ map { return 1 if $_ =~ /$regex/ } keys %{ $record };
+ }
+
+ if ( not $keys_only ) {
+ map { return 1 if $record->{ $_ } =~ /$regex/ } keys %{ $record };
+ }
+ }
+
+ return 0;
+}
+
+
+sub grab_eval
+{
+ # Martin A. Hansen, November 2009.
+
+ # Test if the value of a given record key evaluates according
+ # to a given operator. Returns 1 if eval is OK, else 0.
+
+ my ( $key, # record key
+ $op, # operator
+ $val, # value
+ $record, # hashref
+ ) = @_;
+
+ # Returns boolean.
+
+ if ( defined $record->{ $key } )
+ {
+ return 1 if ( $op eq "<" and $record->{ $key } < $val );
+ return 1 if ( $op eq ">" and $record->{ $key } > $val );
+ return 1 if ( $op eq ">=" and $record->{ $key } >= $val );
+ return 1 if ( $op eq "<=" and $record->{ $key } <= $val );
+ return 1 if ( $op eq "=" and $record->{ $key } == $val );
+ return 1 if ( $op eq "!=" and $record->{ $key } != $val );
+ return 1 if ( $op eq "eq" and $record->{ $key } eq $val );
+ return 1 if ( $op eq "ne" and $record->{ $key } ne $val );
+ }
+
+ return 0;
+}
+
+
sub read_stream
{
# Martin A. Hansen, July 2007.
# 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 );
foreach $line ( @lines )
{
- ( $key, $value ) = split ": ", $line;
+ ( $key, $value ) = split ": ", $line, 2;
$record{ $key } = $value;
}
print STDERR "\nProgram '$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.
+ # Martin A. Hansen, July 2008.
- # 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
- ) = @_;
+ # Cleans out any unused temporary files and directories 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__
projects / biopieces.git / blobdiff