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;
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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
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 "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 ) }
{
@options = qw(
data_in|i=s
+ cols|c=s
num|n=s
+ check|C
);
}
elsif ( $script eq "read_fixedstep" )
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(
percent|p
);
}
- elsif ( $script eq "calc_fixedstep" )
- {
- @options = qw(
- score|S
- log10|L
- );
- }
elsif ( $script eq "transliterate_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(
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(
use_score|u
visibility|V=s
color|c=s
- chunk_size|C=s
+ check|C
);
}
$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 ----
# print STDERR Dumper( \%options );
- $real = "beg|end|word_size|wrap|chunk_size|tile_size|len|prefix_length|mismatches|offset|num|skip|cpus|window_size|step_size";
+ $real = "beg|end|word_size|wrap|tile_size|len|prefix_length|mismatches|offset|num|skip|cpus|window_size|step_size";
foreach $opt ( keys %options )
{
# 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" };
# 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->{ "REC_TYPE" } = "fixed_step";
- $record->{ "CHR" } = $1;
- $record->{ "CHR_BEG" } = $2;
- $record->{ "STEP" } = $3;
- $record->{ "VALS" } = join ";", @{ $entry };
- }
+ $record = Maasha::UCSC::Wiggle::fixedstep2biopiece( $entry );
put_record( $record, $out );
}
+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.
while ( $record = get_record( $in ) )
{
- if ( $fh_out and $entry = record2fasta( $record ) )
+ if ( $fh_out and $entry = Maasha::Fasta::biopiece2fasta( $record ) )
{
Maasha::Fasta::put_entry( $entry, $fh_out, $options->{ "wrap" } );
}
# Returns nothing.
- my ( $record, %fh_hash, $fh_in, $fh_out, $chr, $chr, $beg, $end, $q_id, $block, $entry, $clones, $beg_block, $max, $i );
+ 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 ) )
{
- $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" };
-
- if ( $record->{ "CHR" } and defined $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
- {
- $fh_hash{ $record->{ "CHR" } } = Maasha::Common::write_open( "$BP_TMP/$record->{ 'CHR' }" ) if not exists $fh_hash{ $record->{ "CHR" } };
-
- $fh_out = $fh_hash{ $record->{ "CHR" } };
-
- Maasha::UCSC::bed_put_entry( $record, $fh_out, 5 );
+ if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record, $cols ) ) {
+ Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh_out, $cols, $options->{ 'check' } );
}
}
- map { close $_ } keys %fh_hash;
-
- foreach $chr ( sort keys %fh_hash )
- {
- Maasha::Common::run( "bedSort", "$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 ( $options->{ "score" } ) {
- $clones = $entry->{ 'SCORE' };
- } elsif ( $q_id =~ /_(\d+)$/ ) {
- $clones = $1;
- } else {
- $clones = 1;
- }
-
- if ( $block )
- {
- if ( $beg > $max )
- {
- map { $_ = sprintf( "%.4f", Maasha::Calc::log10( $_ ) ) } @{ $block } if $options->{ "log10" };
-
- $record->{ "CHR" } = $chr;
- $record->{ "CHR_BEG" } = $beg_block;
- $record->{ "STEP" } = 1;
- $record->{ "VALS" } = join ";", @{ $block };
- $record->{ "REC_TYPE" } = "fixed_step";
+ close $fh_out;
- put_record( $record, $out );
+ $file_hash = Maasha::UCSC::BED::bed_file_split_on_chr( $bed_file, $BP_TMP, $cols );
- undef $block;
- }
- else
- {
- for ( $i = $beg - $beg_block; $i < ( $beg - $beg_block ) + ( $end - $beg ); $i++ ) {
- $block->[ $i ] += $clones;
- }
+ unlink $bed_file;
- $max = Maasha::Calc::max( $max, $end );
- }
- }
+ foreach $chr ( sort keys %{ $file_hash } )
+ {
+ $bed_file = $file_hash->{ $chr };
+ $fixedstep_file = "$bed_file.fixedstep";
+
+ Maasha::Common::run( "bed2fixedstep", "< $bed_file > $fixedstep_file" );
- if ( not $block )
- {
- $beg_block = $beg;
- $max = $end;
+ $fh_in = Maasha::Filesys::file_read_open( $fixedstep_file );
- for ( $i = 0; $i < ( $end - $beg ); $i++ ) {
- $block->[ $i ] += $clones;
- }
+ 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;
- map { $_ = sprintf( "%.4f", Maasha::Calc::log10( $_ ) ) } @{ $block } if $options->{ "log10" };
-
- $record->{ "CHR" } = $chr;
- $record->{ "CHR_BEG" } = $beg_block;
- $record->{ "STEP" } = 1;
- $record->{ "VALS" } = join ";", @{ $block };
- $record->{ "REC_TYPE" } = "fixed_step";
-
- put_record( $record, $out );
-
- unlink "$BP_TMP/$chr";
+ unlink $bed_file;
+ unlink $fixedstep_file;
}
}
{
$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" } );
{
put_record( $record, $out ) if not $options->{ "no_stream" };
- if ( $entry = record2fasta( $record ) )
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
{
$seq_type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not $seq_type;
$tmp_in = "$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 ( $entry = record2fasta( $record ) )
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
{
$q_type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not $q_type;
unlink $tmp_in;
- $fh_out = Maasha::Common::read_open( $tmp_out );
+ $fh_out = Maasha::Filesys::file_read_open( $tmp_out );
undef $record;
while ( $record = get_record( $in ) )
{
- if ( $entry = record2fasta( $record ) )
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
{
$type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not $type;
Maasha::Fasta::put_entry( $entry, $fh_out, 80 );
while ( $record = get_record( $in ) )
{
- if ( $entry = record2fasta( $record ) )
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
{
Maasha::Fasta::put_entry( $entry, $fh_out );
while ( $record = get_record( $in ) )
{
- if ( $options->{ "index_name" } and $entry = record2fasta( $record ) )
+ if ( $options->{ "index_name" } and $entry = Maasha::Fasta::biopiece2fasta( $record ) )
{
Maasha::Fasta::put_entry( $entry, $fh_tmp );
while ( $record = get_record( $in ) )
{
- if ( $entry = record2fasta( $record ) ) {
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) {
Maasha::Fasta::put_entry( $entry, $fh, $options->{ "wrap" } );
}
# 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->{ "REC_TYPE" } eq "SOAP" 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;
- $new_record->{ "STRAND" } = $record->{ "STRAND" };
-
- 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" };
while ( $record = get_record( $in ) )
{
- if ( $entry = record2fasta( $record ) ) {
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) {
Maasha::Fasta::put_entry( $entry, $fh_tmp );
}
while ( $record = get_record( $in ) )
{
- if ( $entry = record2fasta( $record ) )
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
{
$entry->[ SEQ ] = Maasha::Solid::seq2color_space( uc $entry->[ SEQ ] );
}
+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.
}
+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.
# Returns nothing.
- my ( $patterns, $pattern, $record, $key, $pos, $op, $val, %lookup_hash );
+ my ( $keys, $vals_only, $keys_only, $invert, $patterns, $pattern, $regex, $record, $key, $op, $val, %lookup_hash, $found );
- if ( $options->{ "patterns" } )
+ $keys = $options->{ 'keys' };
+ $vals_only = $options->{ 'vals_only' };
+ $keys_only = $options->{ 'keys_only' };
+ $invert = $options->{ 'invert' };
+
+ if ( $options->{ 'patterns' } )
{
- $patterns = [ split ",", $options->{ "patterns" } ];
+ $patterns = [ split ",", $options->{ 'patterns' } ];
}
- elsif ( -f $options->{ "patterns_in" } )
+ elsif ( -f $options->{ 'patterns_in' } )
{
- $patterns = Maasha::Patscan::read_patterns( $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 ( -f $options->{ "exact_in" } )
+ elsif ( -f $options->{ 'exact_in' } )
{
- $patterns = Maasha::Patscan::read_patterns( $options->{ "exact_in" } );
+ $patterns = Maasha::Patscan::read_patterns( $options->{ 'exact_in' } );
map { $lookup_hash{ $_ } = 1 } @{ $patterns };
undef $patterns;
}
-
- if ( $options->{ "eval" } )
+ elsif ( $options->{ 'eval' } )
{
- if ( $options->{ "eval" } =~ /^([^><=! ]+)\s*(>=|<=|>|<|=|!=|eq|ne)\s*(.+)$/ )
+ if ( $options->{ 'eval' } =~ /^([^><=! ]+)\s*(>=|<=|>|<|=|!=|eq|ne)\s*(.+)$/ )
{
$key = $1;
$op = $2;
while ( $record = get_record( $in ) )
{
- $pos = -1;
-
- if ( %lookup_hash )
- {
- if ( $options->{ "keys" } )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( exists $lookup_hash{ $record->{ $key } } )
- {
- $pos = 1;
- goto FOUND;
- }
- }
- }
- 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;
- }
- }
- }
- }
- }
- elsif ( $patterns )
- {
- foreach $pattern ( @{ $patterns } )
- {
- if ( $options->{ "keys" } )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- $pos = index $record->{ $key }, $pattern;
-
- goto FOUND if $pos >= 0;
- }
- }
- 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;
- }
- }
- }
- }
- }
- elsif ( $options->{ "regex" } )
- {
- if ( $options->{ "keys" } )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( $options->{ "case_insensitive" } ) {
- $pos = 1 if $record->{ $key } =~ /$options->{'regex'}/i;
- } else {
- $pos = 1 if $record->{ $key } =~ /$options->{'regex'}/;
- }
+ $found = 0;
- goto FOUND if $pos >= 0;
- }
- }
- 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;
- }
-
- 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'}/;
- }
-
- goto FOUND if $pos >= 0;
- }
- }
- }
- }
- elsif ( $options->{ "eval" } )
- {
- 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;
- }
- }
+ 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 );
}
- FOUND:
-
- 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 );
+ 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;
- }
- map { $eval_val =~ s/\Q$_\E/$record->{ $_ }/g } keys %{ $record };
+ if ( not @keys )
+ {
+ @keys = split /\s+|\+|-|\*|\/|\*\*/, $eval_val;
- $record->{ $eval_key } = eval "$eval_val" or Maasha::Common::error( "eval failed -> $@" );
+ @keys = grep { exists $record->{ $_ } } @keys;
+ }
+
+ map { $eval_val =~ s/\Q$_\E/$record->{ $_ }/g } @keys;
+
+ $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 );
# Returns nothing.
- my ( $record, $file, $wib_file, $wig_file, $wib_dir, $fh_out, $i, $first, $format, $type, $columns, $append, $vals );
+ 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 ( $record->{ "REC_TYPE" } eq "fixed_step" )
{
- $vals = $record->{ "VALS" };
- $vals =~ tr/;/\n/;
-
- print $fh_out "fixedStep chrom=$record->{ 'CHR' } start=$record->{ 'CHR_BEG' } step=$record->{ 'STEP' }\n";
- print $fh_out "$vals\n";
+ $format = "WIGGLE";
- $format = "WIGGLE" if not $format;
+ if ( $entry = Maasha::UCSC::Wiggle::biopiece2fixedstep( $record ) ) {
+ Maasha::UCSC::Wiggle::fixedstep_entry_put( $entry, $fh_out );
+ }
}
elsif ( $record->{ "REC_TYPE" } eq "PSL" )
{
+ $format = "PSL";
+
Maasha::UCSC::psl_put_header( $fh_out ) if $first;
Maasha::UCSC::psl_put_entry( $record, $fh_out );
$first = 0;
-
- $format = "PSL" if not $format;
}
elsif ( $record->{ "REC_TYPE" } eq "BED" and $record->{ "SEC_STRUCT" } )
{
# chrom chromStart chromEnd name score strand size secStr conf
+ $format = "BED_SS";
+
print $fh_out join ( "\t",
$record->{ "CHR" },
$record->{ "CHR_BEG" },
$record->{ "SEC_STRUCT" },
$record->{ "CONF" },
), "\n";
-
- $format = "BED_SS" if not $format;
}
elsif ( $record->{ "REC_TYPE" } eq "BED" )
{
- Maasha::UCSC::bed_put_entry( $record, $fh_out, $record->{ "BED_COLS" } );
+ $format = "BED";
+ $columns = $record->{ "BED_COLS" };
- $format = "BED" if not $format;
- $columns = $record->{ "BED_COLS" } 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 "PATSCAN" and $record->{ "CHR" } )
{
- Maasha::UCSC::bed_put_entry( $record, $fh_out, 6 );
+ $format = "BED";
+ $columns = 6;
- $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";
+ $columns = 6;
- $format = "BED" if not $format;
- $columns = 6 if not $columns;
+ $record->{ "SCORE" } = $record->{ "BIT_SCORE" } * 1000;
- 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";
+ $columns = 6;
- $format = "BED" if not $format;
- $columns = 6 if not $columns;
-
- Maasha::UCSC::bed_put_entry( $record, $fh_out, 6 );
+ if ( $entry = Maasha::UCSC::BED::biopiece2bed( $record, $columns ) ) {
+ Maasha::UCSC::BED::bed_entry_put( $entry, $fh_out, $columns, $options->{ 'check' } );
+ }
}
if ( $i == $options->{ "chunk_size" } )
}
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 );
}
unlink $file;
- Maasha::UCSC::update_my_tracks( $options, $type );
+ Maasha::UCSC::ucsc_update_config( $options, $type );
}
}
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-sub record2fasta
+sub grab_lookup
{
- # Martin A. Hansen, July 2008.
+ # 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
+ ) = @_;
- # Given a biopiece record converts it to a FASTA record.
- # If no generic SEQ or SEQ_NAME is found, the Q_* and S_* are
- # tried in that order.
+ # Returns boolean.
- my ( $record, # record
+ 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 a tuple.
+ # Returns boolean.
+
+ my ( $pattern );
- my ( $seq_name, $seq );
+ 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 };
+ }
- $seq_name = $record->{ "SEQ_NAME" } || $record->{ "Q_ID" } || $record->{ "S_ID" };
- $seq = $record->{ "SEQ" } || $record->{ "Q_SEQ" } || $record->{ "S_SEQ" };
+ if ( not $keys_only ) {
+ map { return 1 if index( $record->{ $_ }, $pattern ) >= 0 } keys %{ $record };
+ }
+ }
+ }
- if ( defined $seq_name and defined $seq ) {
- return wantarray ? ( $seq_name, $seq ) : [ $seq_name, $seq ];
- } else {
- return;
+ 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;
}
projects / biopieces.git / blobdiff