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Changeset 258

Timestamp:

09/08/09 11:32:56 (3 months ago)

Author:

cholt

Message:

better iprscan wrapper

Files:

MPI/mpi_iprscan (modified) (7 diffs)
lib/Process/IPRchunk.pm (modified) (8 diffs)
lib/Process/MpiTiers.pm (modified) (2 diffs)
lib/iprscan (added)
lib/iprscan/runlog.pm (added)

Legend:

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

MPI/mpi_iprscan

r256	r258
168	168
169	169	#---global variables
170		my %OPT;
	170	my %CTL_OPT;
	171	my @appl;
	172
171	173	my $root = 0; #define root node (only changed for debugging)
172	174
173	175	#---Process options on the command line
174		my $infile;
175		my $outfile;
176		my @appl;
177		my $chpc;
178		my $cli; #always enabled, just here for implementation
179
180		GetOptions("i=s" => \$infile,
181		"o=s" => \$outfile,
182		"appl=s" => \@appl,
183		"chpc" => \$chpc, #hidden option used on the CHPC's computer farm
184		"cli" => \$cli, #just used to strip off the option
	176	GetOptions("i=s" => \$CTL_OPT{infile},
	177	"o=s" => \$CTL_OPT{outfile},
	178	"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
	187	"cli" => \$CTL_OPT{cli}, #just used to strip off the option
185	188	);
186	189
187		$main::quiet = 1; #suppress status messages
	190	$main::quiet = 1 unless($CTL_OPT{verbose}); #suppress status messages
188	191
189	192	if(! @appl){
…	…
204	207	}
205	208
206		#build localized database for each node
207		if($chpc && ! -e "$TMP/iprscan/data/ok"){
	209	$CTL_OPT{appl} = \@appl; #apply apps to CTL_OPT
	210
	211	#build localized iprscan database for each node
	212	if($CTL_OPT{chpc} && ! -e "$TMP/iprscan/data/ok"){
208	213	my $lock = new File::NFSLock("$TMP/.iprscan_lock", 'EX', 1200, 1205);
209	214
…	…
278	283	#---test command line options here
279	284	#test input files existance
280		if($~~infile && ! -e $infile~~){
281		die "ERROR: The input file \'$~~infile~~\' does not exist.\n";
	285	if($CTL_OPT{infile} && ! -e $CTL_OPT{infile}){
	286	die "ERROR: The input file \'$CTL_OPT{infile}\' does not exist.\n";
282	287	}
283	288
…	…
286	291	my $exe = "$EXE -cli";
287	292	my $command = "$exe " . join(' ', @ARGV);
288		$command .= " -appl " . join(" -appl ", @appl) if(@appl);
289		$command .= " -i $tfile" if($infile); #test options on dummy file
	293	$command .= " -nocrc" if($CTL_OPT{nocrc});
	294	$command .= " -seqtype $CTL_OPT{seqtype}" if(defined $CTL_OPT{seqtype});
	295	$command .= " -trtable $CTL_OPT{trtable}" if(defined $CTL_OPT{trtable});
	296	$command .= " -goterms" if($CTL_OPT{goterms});
	297	$command .= " -iprlookup" if($CTL_OPT{iprlookup});
	298	$command .= " -format $CTL_OPT{format}" if(defined $CTL_OPT{format});
	299	$command .= " -appl " . join(" -appl ", @{$CTL_OPT{appl}}) if(@{$CTL_OPT{appl}});
	300	$command .= " -i $tfile" if($CTL_OPT{infile}); #test options on dummy file
290	301	open(my $PAR, "$command 2>&1 \|");
291	302	my @err = <$PAR>;
…	…
314	325	#---main code for distribution of mpi data starts here
315	326
316		my ($name) = $~~infile~~ =~ /([^\/]+)$/;
317		$name = $~~outfile if($outfile~~);
	327	my ($name) = $CTL_OPT{infile} =~ /([^\/]+)$/;
	328	$name = $CTL_OPT{outfile} if($CTL_OPT{outfile});
318	329
319	330	my $DS_CTL = new basiclog("$name.log");
320		my $iterator = new Iterator::Fasta($~~infile~~);
	331	my $iterator = new Iterator::Fasta($CTL_OPT{infile});
321	332
322	333	#thread for root node to do other things than just manage mpi
…	…
367	378	my $tier;
368	379	while (my $fasta = $iterator->nextFasta() \|\| shift @failed){
369		$tier = Process::MpiTiers->new({fasta => $fasta,
370		appl => \@appl,
371		params => \@ARGV,
372		iprscan => "$EXE -cli",
373		infile => $infile,
374		outfile => $outfile,
375		DS_CTL => $DS_CTL},
	380	$tier = Process::MpiTiers->new({fasta => $fasta,
	381	CTL_OPT => \%CTL_OPT
	382	params => \@ARGV,
	383	iprscan => "$EXE -cli",
	384	DS_CTL => $DS_CTL},
376	385	$root,
377	386	'Process::IPRchunk'
…	…
435	444
436	445	while (my $fasta = $iterator->nextFasta() \|\| shift @failed){
437		$tier = Process::MpiTiers->new({fasta => $fasta,
438		appl => \@appl,
439		params => \@ARGV,
440		iprscan => "$EXE -cli",
441		infile => $infile,
442		outfile => $outfile,
443		DS_CTL => $DS_CTL},
444		$who,
445		'Process::IPRchunk'
446		);
	446	$tier = Process::MpiTiers->new({fasta => $fasta,
	447	CTL_OPT => \%CTL_OPT
	448	params => \@ARGV,
	449	iprscan => "$EXE -cli",
	450	DS_CTL => $DS_CTL},
	451	$who,
	452	'Process::IPRchunk'
	453	);
447	454
448	455	last if(! $tier->terminated);

lib/Process/IPRchunk.pm

r256	r258
116	116	#===
117	117
118		my ($outname) = $VARS->{infile} =~ /([^\/]+)$/;
119		$outname = $VARS->{outfile} if($VARS->{outfile});
	118	my ($outname) = $VARS->{CTL_OPT}{infile} =~ /([^\/]+)$/;
	119	$outname = $VARS->{CTL_OPT}{outfile} if($VARS->{outfile});
120	120
121	121	$VARS->{seq_id} = Fasta::getSeqID(\$VARS->{fasta});
122	122	$VARS->{safe_id} = Fasta::seqID2SafeID($VARS->{seq_id});
123		$VARS->{c_flag} = $VARS->{DS_CTL}->continue_flag($VARS->{seq_id});
124
125		my $failed .= "$outname.failed/".$VARS->{safe_id}.".fasta";
126
127		if(! $VARS->{c_flag}){
128		warn "WARNING: ".$VARS->{seq_id} ."failed 2 time and will not be tried again\n",
129		"The fasta sequence will be saved for debugging in $failed\n";
130
131		mkdir("$outname.failed") if(! -d "$outname.failed");
132
133		open(my $OUT, ">$failed");
134		print $OUT $VARS->{fasta};
135		close($OUT);
136		$VARS->{DS_CTL}->add_entry($VARS->{seq_id}, 'DIED_PERMANENT');
137		}
138		else{
139		unlink($failed) if(-e $failed); #remove old failed
140		}
141
142		$VARS->{DS_CTL}->add_entry($VARS->{seq_id}, 'STARTED');
	123
	124	#set up base and void directories for output
	125	($VARS->{out_dir}, $VARS->{the_void}) = $VARS->{DS_CTL}->seq_dirs($VARS->{seq_id});
	126
	127	#contig combined output file
	128	$VARS->{cfile} = $VARS->{out_dir}."/".$VARS->{safe_id}.".ipr";
	129
	130	#===
	131	$status = 'trying to build/process the run.log file';
	132	#===
	133
	134	$VARS->{LOG} = iprscan::runlog->new($VARS->{CTL_OPT},
	135	{seq_id => $VARS->{seq_id},
	136	seq_length => length(${$VARS->{q_seq_ref}}),
	137	out_dir => $VARS->{out_dir},
	138	the_void => $VARS->{the_void},
	139	fasta_ref => \$VARS->{fasta}},
	140	$VARS->{the_void}."/run.log"
	141	);
	142
	143	($VARS->{c_flag}, my $message) = $VARS->{LOG}->get_continue_flag();
	144	$VARS->{DS_CTL}->add_entry($VARS->{seq_id}, $VARS->{out_dir}, $message);
	145	if($VARS->{c_flag} == 0){
	146	my $cfile = $VARS->{c_flag};
	147	die "ERROR: Can't find $cfile yet iprscan::runlog says the contig is finished\n"
	148	if(! -e $cfile);
	149
	150	my $lock = new File::NFSLock(".iprscan_lock", 'EX', 40, 40);
	151	my $outfile = $VARS->{CTL_OPT}{outfile};
	152
	153	my $FH;
	154	if($outfile){
	155	open($FH, ">> $outfile");
	156	}
	157	else{
	158	open($FH, ">&STDOUT");
	159	}
	160
	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 $cfile;
	168	}
	169
	170	close($FH);
	171	close($CFH);
	172
	173	$lock->unlock;
	174	}
143	175	}
144	176	catch Error::Simple with {
…	…
287	319	if ($flag eq 'load') {
288	320	#-------------------------CHUNKER
289		foreach my $app (@{$VARS->{appl}}) {
	321	foreach my $app (@{$VARS->{CTL_OPT}{appl}}) {
290	322	$VARS->{app} = $app;
291	323	my $chunk = new Process::IPRchunk($level, $VARS);
…	…
296	328	elsif ($flag eq 'init') {
297	329	#------------------------ARGS_IN
298		@args = (qw{safe_fasta
	330	@args = (qw{CTL_OPT
	331	safe_fasta
299	332	app
300	333	params
301	334	iprscan
	335	the_void
302	336	}
303	337	);
…	…
306	340	elsif ($flag eq 'run') {
307	341	#-------------------------CODE
	342	my %CTL_OPT = %{$VARS->{CTL_OPT}};
308	343	my $safe_fasta = $VARS->{safe_fasta};
309	344	my $app = $VARS->{app};
310	345	my $params = $VARS->{params};
311	346	my $iprscan = $VARS->{iprscan};
	347	my $the_void = $VARS->{the_void};
312	348
313	349	#make files
314	350	my (undef, $ifile) = tempfile();
315		my ~~(undef, $ofile) = tempfile()~~;
	351	my $ofile = "$the_void/$CTL_OPT{safe_id}.$app";
316	352	FastaFile::writeFile($safe_fasta, $ifile);
317	353
318	354	#build command
319		my $command = $iprscan . " " . join(' ', @$params);
	355	my $command = $iprscan;
	356	$command .= " -nocrc" if($CTL_OPT{nocrc});
	357	$command .= " -seqtype $CTL_OPT{seqtype}" if(defined $CTL_OPT{seqtype});
	358	$command .= " -trtable $CTL_OPT{trtable}" if(defined $CTL_OPT{trtable});
	359	$command .= " -goterms" if($CTL_OPT{goterms});
	360	$command .= " -iprlookup" if($CTL_OPT{iprlookup});
	361	$command .= " -format $CTL_OPT{format}" if(defined $CTL_OPT{format});
	362	$command .= " " . join(' ', @$params);
320	363	$command .= " -appl $app -i $ifile -o $ofile";
321	364
322	365	my $w = new Widget::iprscan();
323		print STDERR "running iprscan $app...\n" unless($main::quiet);
324		$w->run($command);
	366	if(-e $ofile){
	367	print STDERR "rereading $ofile...\n" unless($main::quiet);
	368	}
	369	else{
	370	print STDERR "running iprscan $app...\n" unless($main::quiet);
	371	$w->run($command);
	372	}
325	373
326	374	unlink($ifile);
…	…
331	379	}
332	380	close($IN);
333		~~unlink($ofile);~~
334	381	#-------------------------CODE
335	382
…	…
354	401	elsif ($flag eq 'init') {
355	402	#------------------------ARGS_IN
356		@args = (qw{outfile},
357		@{$VARS->{appl}}
	403	@args = (qw{CTL_OPT
	404	cfile
	405	outfile
	406	},
	407	@{$VARS->{CTL_OPT}{appl}}
358	408	);
359	409	#------------------------ARGS_IN
…	…
361	411	elsif ($flag eq 'run') {
362	412	#-------------------------CODE
363		my $outfile = $VARS->{outfile};
	413	my $cfile = $VARS->{cfile}; #combined contig output file
	414	my $outfile = $VARS->{outfile}; #combined every contig output file
364	415
365	416	my $lock = new File::NFSLock(".iprscan_lock", 'EX', 40, 40);
…	…
373	424	}
374	425
	426	my $CFH;
	427	open($CFH, "> $cfile");
	428
375	429	while(my $key = each %{$VARS}){
376	430	next if($key eq 'outfile');
377	431	print $FH $VARS->{$key};
	432	print $CFH $cfile;
378	433	}
	434
379	435	close($FH);
	436	close($CFH);
380	437
381	438	$lock->unlock;

lib/Process/MpiTiers.pm

r256	r258
4	4
5	5	use strict;
	6	use FindBin;
	7	use lib "$FindBin::Bin/../lib";
	8	use lib "$FindBin::Bin/../perl/lib";
6	9	use Error qw(:try);
7	10	use Error::Simple;
…	…
43	46	#optionaly override chunk type
44	47	$self->{CHUNK_REF} = shift @args \|\| "Process::MpiChunk";
	48	require $self->{CHUNK_REF};
45	49	$self->{CHUNK_REF} = new $self->{CHUNK_REF}; #turn into object
46	50

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