--- /dev/null
+#!/usr/bin/env perl -w
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Monitor status running Biopieces.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use strict;
+use Maasha::Biopieces;
+use Maasha::Common;
+use Maasha::Filesys;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $allowed, @files, $file, $user, $pid, $script, $info, $time0, $time1, $args, $du, @table );
+
+$allowed = "USER,PID,%CPU,%MEM,TMP_DIR,START_TIME,RUN_TIME,COMMAND";
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'time', short => 't', type => 'uint', mandatory => 'no', default => 5, allowed => undef, disallowed => 0 },
+ { long => 'sort', short => 's', type => 'string', mandatory => 'no', default => '%CPU', allowed => $allowed, disallowed => undef },
+ { long => 'user', short => 'u', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ ]
+);
+
+while ( 1 )
+{
+ system( "clear" );
+
+ undef @table;
+
+ @files = Maasha::Filesys::ls_files( $ENV{ 'BP_TMP' } );
+ @files = grep /\.status$/, @files;
+
+ if ( $options->{ 'user' } ) {
+ @files = grep /$options->{ 'user' }/, @files;
+ }
+
+ foreach $file ( @files )
+ {
+ ( $user, $script, $pid ) = split /\./, $file;
+
+ if ( $info = process_info_mac( $pid ) )
+ {
+ ( $time0, $args, $du ) = get_status_info( $file );
+
+ $info->{ 'START_TIME' } = $time0;
+ $info->{ 'RUN_TIME' } = Maasha::Common::time_stamp_diff( $time0, Maasha::Common::time_stamp() );
+ $info->{ 'TMP_DIR' } = $du || "N/A";
+ $info->{ 'COMMAND' } = "$script $args";
+
+ push @table, $info;
+ }
+ else
+ {
+ print STDERR "Removing stale file: $file\n";
+ unlink $file;
+ }
+ }
+
+ if ( $options->{ 'sort' } =~ /^(USER|TMP_DIR|START_TIME|RUN_TIME|COMMAND)$/ ) {
+ @table = sort { $a->{ $options->{ 'sort' } } cmp $b->{ $options->{ 'sort' } } } @table;
+ } else {
+ @table = sort { $a->{ $options->{ 'sort' } } <=> $b->{ $options->{ 'sort' } } } @table;
+ }
+
+ print join( "\t", 'USER', 'PID', '%CPU', '%MEM', 'TMP_DIR', 'START_TIME ', 'RUN_TIME', 'COMMAND' ), "\n";
+ print join( "\t", $_->{ 'USER' }, $_->{ 'PID' }, $_->{ '%CPU' }, $_->{ '%MEM' }, $_->{ 'TMP_DIR' }, $_->{ 'START_TIME' }, $_->{ 'RUN_TIME' }, $_->{ 'COMMAND' } ), "\n" foreach @table;
+
+ sleep $options->{ 'time' };
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub process_info_mac
+{
+ # Martin A. Hansen, June 2009.
+
+ # Get process info for a given process given a PID by
+ # calling ps aux on a Mac.
+
+ # ps aux:
+ # USER PID %CPU %MEM VSZ RSS TT STAT STARTED TIME COMMAND
+
+ my ( $pid, # process id
+ ) = @_;
+
+ # Returns a hashref
+
+ my ( @processes, $process, @fields, %info_hash, $hour, $min, $ampm );
+
+ @processes = `ps aux`;
+
+ shift @processes;
+
+ foreach $process ( @processes )
+ {
+ @fields = split " ", $process;
+
+ if ( $fields[ 1 ] == $pid )
+ {
+ %info_hash = (
+ "USER" => $fields[ 0 ],
+ "PID" => $fields[ 1 ],
+ "%CPU" => $fields[ 2 ],
+ "%MEM" => $fields[ 3 ],
+ "VSZ" => $fields[ 4 ],
+ "RSS" => $fields[ 5 ],
+ "TT" => $fields[ 6 ],
+ "STAT" => $fields[ 7 ],
+ "STARTED" => $fields[ 8 ],
+ "TIME" => $fields[ 9 ],
+ "COMMAND" => $fields[ 10 ],
+ );
+
+ if ( $info_hash{ 'STARTED' } =~ /^(\d+):(\d+)(AM|PM)$/ )
+ {
+ $hour = $1;
+ $min = $2;
+ $ampm = $3;
+
+ if ( $ampm eq "PM" ) {
+ $hour += 12;
+ }
+
+ $info_hash{ 'STARTED' } = "$hour:$min";
+ }
+
+ return wantarray ? %info_hash : \%info_hash;
+ }
+ }
+
+ return;
+}
+
+
+sub get_status_info
+{
+ my ( $file, #
+ ) = @_;
+
+ my ( $fh, $line, $time, $args, $tmp_dir, $du );
+
+ $fh = Maasha::Filesys::file_read_open( $file );
+ $line = <$fh>;
+ close $fh;
+
+ chomp $line;
+
+ ( $time, $args, $tmp_dir ) = split ";", $line;
+
+ if ( $tmp_dir and -d $tmp_dir )
+ {
+ $du = `du -sh $tmp_dir`;
+
+ chomp $du;
+
+ $du =~ s/\s.*//;
+ }
+
+ return wantarray ? ( $time, $args, $du ) : [ $time, $args, $du ];
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
$options = Maasha::Biopieces::parse_options(
[
- { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
- { long => 'occ', short => 'c', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'tile_size', short => 't', type => 'uint', mandatory => 'no', default => 11, allowed => undef, disallowed => 0 },
- { long => 'step_size', short => 's', type => 'uint', mandatory => 'no', default => 11, allowed => undef, disallowed => 0 },
- { long => 'min_identity', short => 'm', type => 'uint', mandatory => 'no', default => 90, allowed => undef, disallowed => 0 },
- { long => 'min_score', short => 'M', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
- { long => 'one_off', short => 'o', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { long => 'fast_map', short => 'f', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'occ', short => 'c', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'intron_max', short => 'i', type => 'uint', mandatory => 'no', default => 750000, allowed => undef, disallowed => undef },
+ { long => 'tile_size', short => 't', type => 'uint', mandatory => 'no', default => 11, allowed => undef, disallowed => 0 },
+ { long => 'step_size', short => 's', type => 'uint', mandatory => 'no', default => 11, allowed => undef, disallowed => 0 },
+ { long => 'min_identity', short => 'm', type => 'uint', mandatory => 'no', default => 90, allowed => undef, disallowed => 0 },
+ { long => 'min_score', short => 'M', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'one_off', short => 'o', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
]
);
$blat_args .= " -minIdentity=$options->{ 'min_identity' }";
$blat_args .= " -minScore=$options->{ 'min_score' }";
$blat_args .= " -stepSize=$options->{ 'step_size' }";
+$blat_args .= " -maxIntron=$options->{ 'intron_max' }";
+$blat_args .= " -fastMap" if $options->{ 'fast_map' };
# $blat_args .= " -ooc=" . Maasha::Config::genome_blat_ooc( $options->{ "genome" }, 11 ) if $options->{ 'ooc' };
$tmp_dir = Maasha::Biopieces::get_tmpdir();
$num = 1;
- while ( $record = Maasha::UCSC::PSL::psl_get_entry( $data_in ) )
+ while ( $entry = Maasha::UCSC::PSL::psl_entry_get( $data_in ) )
{
- Maasha::Biopieces::put_record( $record, $out );
+ if ( $record = Maasha::UCSC::PSL::psl2biopiece( $entry ) )
+ {
+ Maasha::Biopieces::put_record( $record, $out );
- last if $options->{ "num" } and $num == $options->{ "num" };
+ last if $options->{ "num" } and $num == $options->{ "num" };
- $num++;
+ $num++;
+ }
}
close $data_in;
--- /dev/null
+#!/usr/bin/env ruby
+
+require 'Maasha/biopieces'
+require 'getoptlong'
+
+options = GetoptLong.new(
+ [ '--help', '-?', GetoptLong::NO_ARGUMENT ],
+ [ '--stream_in', '-I', GetoptLong::REQUIRED_ARGUMENT ],
+ [ '--stream_out', '-O', GetoptLong::REQUIRED_ARGUMENT ],
+ [ '--verbose', '-v', GetoptLong::NO_ARGUMENT ]
+)
+
+if ARGV.length == 0 then
+ biopiece = $0.split( "/" ).last
+ exec "print_wiki --data_in #{ ENV[ 'BP_DIR' ] }/bp_usage/#{ biopiece }.wiki"
+end
+
+options.each do | opt, arg |
+ puts "option: #{ opt } argument: #{ arg }"
+
+ case opt
+ when '--help'
+ biopiece = $0.split( "/" ).last
+ exec "print_wiki --data_in #{ ENV[ 'BP_DIR' ] }/bp_usage/#{ biopiece }.wiki --help"
+ when '--stream_in'
+ puts "Stream in"
+ stream = File.open( arg )
+ when '--stream_out'
+ puts "Stream out"
+ when '--verbose'
+ puts "blababnlbalbalbalbalab"
+ end
+end
+
+bp_stream = BioPieces.new( "test.stream" )
+
+puts bp_stream.record_get
### The following directories hold the biopiece libraries, modules, gems, etc - one per programming language.
-export BP_PERL="$BP_DIR/code_perl" # Direcotry with Perl code.
-export BP_C="$BP_DIR/code_c" # Direcotry with C code.
-export BP_PYTHON="$BP_DIR/code_python" # Direcotry with Pyton code.
-export BP_RUBY="$BP_DIR/code_ruby" # Direcotry with Ruby code.
+export BP_PERL="$BP_DIR/code_perl" # Direcotory with Perl code.
+export BP_C="$BP_DIR/code_c" # Direcotory with C code.
+export BP_PYTHON="$BP_DIR/code_python" # Direcotory with Pyton code.
+export BP_RUBY="$BP_DIR/code_ruby" # Direcotory with Ruby code.
### Here we add the biopiece variable to the existing PATH.
{
# Martin A. Hansen, May 2009
- #
+ # Parses and checks options for Biopieces.
+
+ # First the argument list is checked for duplicates and then
+ # options are parsed from ARGV after which it is checked if
+ # the Biopieces usage information should be printed. Finally,
+ # all options from ARGV are checked according to the argument list.
my ( $arg_list, # data structure with argument description
) = @_;
if ( exists $options->{ 'help' } ) {
`print_wiki --data_in=$wiki --help`;
- } elsif ( $script =~ /^(list_biopieces|list_genomes)$/ ) {
+ } elsif ( $script =~ /^(list_biopieces|list_genomes|biostat)$/ ) {
return;
} else {
`print_wiki --data_in=$wiki`;
}
-sub run_time
-{
- # Martin A. Hansen, May 2009.
-
- # Returns a precision timestamp for calculating
- # run time.
-
- return Maasha::Common::get_time_hires();
-}
-
-
-sub run_time_print
-{
- # Martin A. Hansen, May 2009
-
- # Print the run time to STDERR for the current script if
- # the verbose switch is set in the option hash.
-
- my ( $t0, # run time begin
- $t1, # run time end
- $options, # options hash
- ) = @_;
-
- # Returns nothing
-
- my $script = Maasha::Common::get_scriptname();
-
- print STDERR "Program: $script" . ( " " x ( 25 - length( $script ) ) ) . sprintf( "Run time: %.4f\n", ( $t1 - $t0 ) ) if $options->{ 'verbose' };
-
-}
-
-
sub get_tmpdir
{
# Martin A. Hansen, April 2008.
$min0 = $5;
$sec0 = $6;
+ $sec0 += $day0 * 24 * 60 * 60;
$sec0 += $hour0 * 60 * 60;;
$sec0 += $min0 * 60;
$min1 = $5;
$sec1 = $6;
+ $sec1 += $day1 * 24 * 60 * 60;
$sec1 += $hour1 * 60 * 60;;
$sec1 += $min1 * 60;
class BioPieces
RECORD_DELIMITER = "\n---\n"
-
+
class Record
attr_reader :__hash__
projects / biopieces.git / commitdiff