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Changeset 259

Timestamp:

09/08/09 16:43:05 (3 months ago)

Author:

cholt

Message:

mpi_iprscan more maker like behavior

Files:

MPI/mpi_iprscan (modified) (10 diffs)
lib/Process/IPRchunk.pm (modified) (13 diffs)
lib/Process/MpiTiers.pm (modified) (1 diff)
lib/basiclog.pm (added)
lib/iprscan/runlog.pm (modified) (10 diffs)

Legend:

: Unmodified
: Added
: Removed
: Modified
: Copied
: Moved

MPI/mpi_iprscan

r258	r259
14	14	use threads;
15	15	use threads::shared;
16		~~use Cwd;~~
17	16
18	17	BEGIN{
…	…
34	33	#what to do on ^C
35	34	$SIG{'INT'} = sub {
36		print STDERR "\n\n~~Maker~~ aborted by user!!\n\n";
	35	print STDERR "\n\nmpi_iprscan aborted by user!!\n\n";
37	36	my @threads = threads->list;
38	37	foreach my $thr (@threads){
…	…
75	74	use Iterator::Fasta;
76	75	use Fasta;
77		use ~~basiclog~~;
	76	use ds_utility;
78	77	use Error qw(:try);
79	78	use Error::Simple;
80	79	use Process::IPRchunk;
81	80	use Process::MpiTiers;
	81	use Process::IPRchunk;
82	82	use Parallel::MPIcar qw(:all);
	83	use iprscan::runlog;
83	84
84	85	unless($threads::VERSION >= 1.67){
…	…
173	174	my $root = 0; #define root node (only changed for debugging)
174	175
	176	$CTL_OPT{retry} = 2;
	177	$CTL_OPT{seqtype} = 'p'; #default
	178
175	179	#---Process options on the command line
176	180	GetOptions("i=s" => \$CTL_OPT{infile},
177	181	"o=s" => \$CTL_OPT{outfile},
178	182	"appl=s" => \@appl,
179		"nocrc" => $CTL_OPT{nocrc},
180		"seqtype=s" => $CTL_OPT{seqtype},
181		"trtable=i" => $CTL_OPT{trtable},
182		"goterms" => $CTL_OPT{goterms},
183		"iprlookup" => $CTL_OPT{iprlookup},
184		"format=s" => $CTL_OPT{format},
185		"verbose" => $CTL_OPT{verbose},
186		"chpc" => \$CTL_OPT{chpc}, #hidden option used on the CHPC's computer farm
	183	"nocrc" => \$CTL_OPT{nocrc},
	184	"seqtype=s" => \$CTL_OPT{seqtype},
	185	"trtable=i" => \$CTL_OPT{trtable},
	186	"goterms" => \$CTL_OPT{goterms},
	187	"iprlookup" => \$CTL_OPT{iprlookup},
	188	"format=s" => \$CTL_OPT{format},
	189	"verbose" => \$CTL_OPT{verbose},
	190	"retry" => \$CTL_OPT{retry},
	191	"chpc" => \$CTL_OPT{chpc}, #hidden option for retrying
187	192	"cli" => \$CTL_OPT{cli}, #just used to strip off the option
188	193	);
…	…
208	213
209	214	$CTL_OPT{appl} = \@appl; #apply apps to CTL_OPT
	215
	216	#build out_base and out_name for datastore
	217	$CTL_OPT{out_name} = ($CTL_OPT{outfile}) ? $CTL_OPT{outfile} : $CTL_OPT{infile};
	218	$CTL_OPT{out_name} =~ /([^\/]+)$/;
	219	$CTL_OPT{out_name} = $1;
	220	$CTL_OPT{out_name} =~ s/(.+)\.[^\.]+$/$1/;
	221	$CTL_OPT{out_base} = Cwd::cwd()."/$CTL_OPT{out_name}.iprscan.output";
210	222
211	223	#build localized iprscan database for each node
…	…
297	309	$command .= " -iprlookup" if($CTL_OPT{iprlookup});
298	310	$command .= " -format $CTL_OPT{format}" if(defined $CTL_OPT{format});
	311	$command .= " -verbose" if($CTL_OPT{verbose});
299	312	$command .= " -appl " . join(" -appl ", @{$CTL_OPT{appl}}) if(@{$CTL_OPT{appl}});
300	313	$command .= " -i $tfile" if($CTL_OPT{infile}); #test options on dummy file
…	…
328	341	$name = $CTL_OPT{outfile} if($CTL_OPT{outfile});
329	342
330		my $DS_CTL = new ~~basiclog("$name.log"~~);
	343	my $DS_CTL = new ds_utility(\%CTL_OPT);
331	344	my $iterator = new Iterator::Fasta($CTL_OPT{infile});
332	345
…	…
379	392	while (my $fasta = $iterator->nextFasta() \|\| shift @failed){
380	393	$tier = Process::MpiTiers->new({fasta => $fasta,
381		CTL_OPT => \%CTL_OPT
	394	CTL_OPT => \%CTL_OPT,
382	395	params => \@ARGV,
383	396	iprscan => "$EXE -cli",
…	…
445	458	while (my $fasta = $iterator->nextFasta() \|\| shift @failed){
446	459	$tier = Process::MpiTiers->new({fasta => $fasta,
447		CTL_OPT => \%CTL_OPT
	460	CTL_OPT => \%CTL_OPT,
448	461	params => \@ARGV,
449	462	iprscan => "$EXE -cli",
…	…
615	628	$thr->detach() unless($thr->is_detached);
616	629
617		print STDERR "\n\n~~Maker is now finished!!!\n\n"~~;
	630	print STDERR "\n\nmpi_iprscan is now finished!!!\n\n" unless($main::quiet);
618	631	}
619	632	#------SECONDARY MPI PROCESSES------

lib/Process/IPRchunk.pm

r258	r259
1		#! /usr/bin/perl -w
2
	1	#! /usr/bin/perl
3	2	package Process::IPRchunk;
4	3
…	…
14	13	use Widget::iprscan;
15	14	use URI::Escape;
	15	use iprscan::runlog;
16	16
17	17	#--set object variables for serialization of data
…	…
134	134	$VARS->{LOG} = iprscan::runlog->new($VARS->{CTL_OPT},
135	135	{seq_id => $VARS->{seq_id},
136		~~seq_length => length(${$VARS->{q_seq_ref}}),~~
137	136	out_dir => $VARS->{out_dir},
138	137	the_void => $VARS->{the_void},
…	…
144	143	$VARS->{DS_CTL}->add_entry($VARS->{seq_id}, $VARS->{out_dir}, $message);
145	144	if($VARS->{c_flag} == 0){
146		my $cfile = $VARS->{c~~_flag~~};
	145	my $cfile = $VARS->{cfile};
147	146	die "ERROR: Can't find $cfile yet iprscan::runlog says the contig is finished\n"
148	147	if(! -e $cfile);
…	…
158	157	open($FH, ">&STDOUT");
159	158	}
	159
	160	#open for reading
	161	open(my $CFH, "< $cfile");
160	162
161		my $CFH;
162		open($CFH, "> $cfile");
163
164		while(my $key = each %{$VARS}){
165		next if($key eq 'outfile');
166		print $FH $VARS->{$key};
167		print $CFH $cfile;
	163	while(my $line = <$CFH>){
	164	print $FH $line;
168	165	}
169	166
…	…
329	326	#------------------------ARGS_IN
330	327	@args = (qw{CTL_OPT
	328	safe_id
331	329	safe_fasta
332	330	app
…	…
334	332	iprscan
335	333	the_void
	334	LOG
336	335	}
337	336	);
…	…
342	341	my %CTL_OPT = %{$VARS->{CTL_OPT}};
343	342	my $safe_fasta = $VARS->{safe_fasta};
	343	my $safe_id = $VARS->{safe_id};
344	344	my $app = $VARS->{app};
345	345	my $params = $VARS->{params};
346	346	my $iprscan = $VARS->{iprscan};
347	347	my $the_void = $VARS->{the_void};
348
	348	my $LOG = $VARS->{LOG};
	349
349	350	#make files
350	351	my (undef, $ifile) = tempfile();
351		my $ofile = "$the_void/$~~CTL_OPT{safe_id}~~.$app";
	352	my $ofile = "$the_void/$safe_id.$app";
352	353	FastaFile::writeFile($safe_fasta, $ifile);
353	354
…	…
360	361	$command .= " -iprlookup" if($CTL_OPT{iprlookup});
361	362	$command .= " -format $CTL_OPT{format}" if(defined $CTL_OPT{format});
	363	$command .= " -verbose" if($CTL_OPT{verbose});
362	364	$command .= " " . join(' ', @$params);
363	365	$command .= " -appl $app -i $ifile -o $ofile";
	366
	367	$LOG->add_entry("STARTED", $ofile, "");
364	368
365	369	my $w = new Widget::iprscan();
…	…
372	376	}
373	377
	378	$LOG->add_entry("FINISHED", $ofile, "");
	379
374	380	unlink($ifile);
375	381	open(my $IN, "< $ofile");
…	…
403	409	@args = (qw{CTL_OPT
404	410	cfile
405		~~outfile~~
406	411	},
407	412	@{$VARS->{CTL_OPT}{appl}}
…	…
411	416	elsif ($flag eq 'run') {
412	417	#-------------------------CODE
	418	my %CTL_OPT = %{$VARS->{CTL_OPT}};
413	419	my $cfile = $VARS->{cfile}; #combined contig output file
414		my $outfile = $~~VARS->~~{outfile}; #combined every contig output file
	420	my $outfile = $CTL_OPT{outfile}; #combined every contig output file
415	421
416	422	my $lock = new File::NFSLock(".iprscan_lock", 'EX', 40, 40);
…	…
427	433	open($CFH, "> $cfile");
428	434
429		~~while(my $key = each %{$VARS~~}){
430		next if(~~$key eq 'outfile'~~);
	435	foreach my $key (@{$CTL_OPT{appl}}){
	436	next if(! defined ($VARS->{$key}));
431	437	print $FH $VARS->{$key};
432		print $CFH $~~cfile~~;
	438	print $CFH $VARS->{$key};
433	439	}
434	440

lib/Process/MpiTiers.pm

r258	r259
46	46	#optionaly override chunk type
47	47	$self->{CHUNK_REF} = shift @args \|\| "Process::MpiChunk";
48		~~require~~ $self->{CHUNK_REF};
49		$self->{CHUNK_REF} = ~~new $self->{CHUNK_REF}~~; #turn into object
	48	eval "require ". $self->{CHUNK_REF};
	49	$self->{CHUNK_REF} = $self->{CHUNK_REF}->new(); #turn into object
50	50
51	51	#setup the tier

lib/iprscan/runlog.pm

r258	r259
1	1	#-------------------------------------------------------------------------------
2		#------ ~~runlog~~ ---------
3		#-------------------------------------------------------------------------------
4		package runlog;
	2	#------ iprscan::runlog ---------
	3	#-------------------------------------------------------------------------------
	4	package iprscan::runlog;
5	5	use strict;
6	6	use vars qw(@ISA @EXPORT $VERSION);
…	…
55	55	print STDERR "\n\n\n--Next Contig--\n\n" unless($main::quiet);
56	56
57		my $min_contig = $self->{CTL_OPTIONS}->{min_contig} \|\| 0;
58		my $length = $self->{params}->{seq_length};
59
60		if($length < $min_contig){#skip if this is a short contig
61		$self->{continue_flag} = -2; #skipped signal is -2
62
63		return 0;
64		}
	57	#my $min_contig = $self->{CTL_OPTIONS}->{min_contig} \|\| 0;
	58	#my $length = $self->{params}->{seq_length};
	59
	60	#if($length < $min_contig){#skip if this is a short contig
	61	# $self->{continue_flag} = -2; #skipped signal is -2
	62	#
	63	# return 0;
	64	#}
65	65
66	66	return 1;
…	…
186	186	$key eq 'goterms' \|\|
187	187	$key eq 'iprlookup' \|\|
188		$key eq 'format' \|\|
	188	$key eq 'format'
189	189	) {
190	190	$rm_key{all}++;
…	…
334	334	my $out_dir = $self->{params}->{out_dir};
335	335	my $fasta_ref = $self->{params}->{fasta_ref};
336		my $length = $self->{params}->{seq_length};
	336	#my $length = $self->{params}->{seq_length};
337	337
338	338	if($flag == 0){
…	…
341	341	"mpi_iprscan will now skip to the next contig.\n",
342	342	"SeqID: $seq_id\n",
343		"Length: $length\n",
	343	#"Length: $length\n",
344	344	"#---------------------------------------------------------------------\n\n\n";
345	345	}
…	…
348	348	"Now starting the contig!!\n",
349	349	"SeqID: $seq_id\n",
350		"Length: $length\n",
	350	#"Length: $length\n",
351	351	"#---------------------------------------------------------------------\n\n\n";
352	352	}
…	…
356	356	"All contig related data will be erased before continuing!!\n",
357	357	"SeqID: $seq_id\n",
358		"Length: $length\n",
	358	#"Length: $length\n",
359	359	"Retry: $die_count!!\n",
360	360	"#---------------------------------------------------------------------\n\n\n";
…	…
364	364	"Now retrying the contig!!\n",
365	365	"SeqID: $seq_id\n",
366		"Length: $length\n",
	366	#"Length: $length\n",
367	367	"Retry: $die_count!!\n",
368	368	"#---------------------------------------------------------------------\n\n\n";
…	…
374	374	"The contig will be stored in a fasta file that you can use for debugging.\n",
375	375	"SeqID: $seq_id\n",
376		"Length: $length\n",
	376	#"Length: $length\n",
377	377	"FASTA: $out_dir/$seq_out_name.died.fasta\n",
378	378	"#---------------------------------------------------------------------\n\n\n";
…	…
386	386	"Skipping the contig because it is too short!!\n",
387	387	"SeqID: $seq_id\n",
388		"Length: $length\n",
	388	#"Length: $length\n",
389	389	"#---------------------------------------------------------------------\n\n\n";
390	390	}

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