$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 "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 ) }
close $in if defined $in;
close $out;
-
- # unset status - missing
- # write log file - missing
}
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(
);
# 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;
}
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 ( $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 = record2fasta( $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" } )
{
$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 = record2fasta( $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";
while ( $record = get_record( $in ) )
{
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+ if ( $entry = record2fasta( $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 );
# 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 = record2fasta( $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_soap_seq
+{
+ # Martin A. Hansen, July 2008.
+
+ # soap sequences in stream against a given file or genome.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $genome, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $line, @fields, $entry );
+
+ $options->{ "seed_size" } ||= 10;
+ $options->{ "mismatches" } ||= 2;
+ $options->{ "gap_size" } ||= 0;
+ $options->{ "cpus" } ||= 1;
+
+ $options->{ "in_file" } = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna" if $options->{ 'genome' };
+
+ $tmp_in = "$BP_TMP/soap_query.seq";
+ $tmp_out = "$BP_TMP/soap.result";
+
+ $fh_out = Maasha::Common::write_open( $tmp_in );
+
+ while ( $record = get_record( $in ) )
+ {
+ if ( $entry = record2fasta( $record ) ) {
+ Maasha::Fasta::put_entry( $entry, $fh_out );
+ }
+
+ put_record( $record, $out );
+ }
+
+ close $fh_out;
+
+ Maasha::Common::run( "soap", "-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 > /dev/null 2>&1", 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.
# 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 = record2fasta( $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 = record2fasta( $record ) ) {
+ Maasha::Fasta::put_entry( $entry, $fh, $options->{ "wrap" } );
}
put_record( $record, $out ) if not $options->{ "no_stream" };
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 );
# 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 = record2fasta( $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 = record2fasta( $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" };
$wig_file = "$options->{ 'table' }.wig";
$wib_file = "$options->{ 'table' }.wib";
- $wib_dir = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'database' }/wib";
+ $wib_dir = "$ENV{ 'HOME' }/ucsc/wib";
Maasha::Common::dir_create_if_not_exists( $wib_dir );
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+sub record2fasta
+{
+ # Martin A. Hansen, July 2008.
+
+ # 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.
+
+ my ( $record, # record
+ ) = @_;
+
+ # Returns a tuple.
+
+ my ( $seq_name, $seq );
+
+ $seq_name = $record->{ "SEQ_NAME" } || $record->{ "Q_ID" } || $record->{ "S_ID" };
+ $seq = $record->{ "SEQ" } || $record->{ "Q_SEQ" } || $record->{ "S_SEQ" };
+
+ if ( defined $seq_name and defined $seq ) {
+ return wantarray ? ( $seq_name, $seq ) : [ $seq_name, $seq ];
+ } else {
+ return;
+ }
+}
+
+
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
+sub clean_tmp
{
- # 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__
+ # Martin A. Hansen, July 2008.
-
-sub script_read_soft
-{
- # Martin A. Hansen, December 2007.
-
- # Read soft format.
- # http://www.ncbi.nlm.nih.gov/geo/info/soft2.html
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
+ # Cleans out any unused temporary files and direcotries 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 );
+ $user = $1;
+ $sid = $2;
+ $pid = $3;
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $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