Commit 6e8a11275ccd2187dae501d352e0677701ed68ff - barrnap

Reorganized executables: made bin/ dir and binaries/$OPSYS/ dirs. Torsten Seemann 9 years ago

6 changed file(s) with 224 addition(s) and 224 deletion(s). Raw diff Collapse all Expand all

-224

~~barrnap~~ less more

0		#!/usr/bin/env perl
1		use strict;
2		use warnings;
3		use Time::Piece;
4		use FindBin;
5
6		# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7		# global variables
8
9		my $EXE = $FindBin::RealScript;
10		my $VERSION = "0.3";
11		my $DESC = "Bacterial/Archaeal Ribosomal RNA Predictor";
12		my $AUTHOR = 'Torsten Seemann <torsten.seemann@monash.edu>';
13		my $URL = 'http://www.vicbioinformatics.com/';
14		my $DBDIR = "$FindBin::RealBin/db";
15		my $OPSYS = $^O;
16		my $NHMMER = "$FindBin::RealBin/binaries/nhmmer.$OPSYS";
17		my %LENG = ("5S_rRNA"=>119, "16S_rRNA"=>1585, "23S_rRNA"=>3232);
18
19		# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
20		# command line options
21
22		my(@Options, $quiet, $kingdom, $threads, $evalue, $lencutoff, $incseq);
23		setOptions();
24
25		# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
26		# check all is well
27
28		msg("This is $EXE $VERSION");
29		msg("Written by $AUTHOR");
30		msg("Obtained from $URL");
31		msg("Detected operating system: $OPSYS");
32
33		if (! -x $NHMMER) {
34		err("No binary for your OS '$OPSYS' is included. If you have one, copy it to $NHMMER.");
35		}
36		msg("Using HMMER binary: $NHMMER");
37
38		#if (! -r "$DATABASE.h3i") {
39		# err("The pressed HMM files are missing. Go to the barnapp folder and type 'make database'");
40		#}
41		#msg("Found database files: $DATABASE.*");
42
43		$threads > 0 or err("Invalid --threads $threads");
44		msg("Will use $threads threads");
45
46		$evalue > 0 or err("Invalid --evalue $evalue");
47		msg("Setting evalue cutoff to $evalue");
48
49		$lencutoff > 0 or err("Invalid --lencutoff $lencutoff");
50		msg("Will tag genes < $lencutoff x full length as partial genes");
51
52		if ($kingdom =~ m/^b/i) {
53		$kingdom = 'bacteria';
54		}
55		elsif ($kingdom =~ m/^a/i) {
56		$kingdom = 'archaea';
57		}
58		else {
59		err("I don't recognise the --kingdom '$kingdom'. Try 'bacteria' or 'archaea'.");
60		}
61
62		my $hmmdb = "$DBDIR/$kingdom.hmm";
63		err("Can't find database: $hmmdb") unless -r $hmmdb;
64		msg("Using database: $hmmdb");
65
66		# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
67		# run the external command
68
69		my $fasta = shift @ARGV;
70		$fasta && -r $fasta or err("Usage: $EXE <file.fasta>");
71
72		msg("Running $NHMMER on $fasta ... please wait");
73		my $cmd = "$NHMMER --cpu $threads -E $evalue --w_length 2000 -o /dev/null --tblout /dev/stdout \Q$hmmdb\E \Q$fasta\E";
74		my @hits = qx($cmd 2>&1);
75
76		# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
77		# process the output
78
79		my @feat;
80		foreach (@hits) {
81		chomp;
82		err("nhmmer failed to run - $_") if m/fail\|error\|core dump\|bus error/i;
83		next if m/^#/; # comment line
84		next if m/^\s*$/; # empty line
85		my @x = split ' ', $_;
86		err("bad line in nhmmer output - @x") unless defined $x[6] and $x[6] =~ m/^\d+$/;
87
88		my($begin,$end,$strand) = $x[6] < $x[7] ? ($x[6],$x[7],'+') : ($x[7],$x[6],'-');
89		my($seqid, $gene, $prod) = ($x[0], $x[2], $x[2]);
90
91		# assumes NAME field in .HMM file is of form "16s_rRNA" etc
92		$prod =~ s/_r/ ribosomal /; # convert the short ID to an English string
93
94		# check for incomplete alignments
95		my $len = $end-$begin+1;
96		if ($len < int($lencutoff * $LENG{$gene}) ) {
97		$prod .= " (partial)";
98		}
99
100		msg("Found:", $gene, $seqid, "L=$len/$LENG{$gene}", "$begin..$end", $strand, $prod);
101		push @feat, [
102		$seqid, "$EXE:$VERSION", 'rRNA', $begin, $end, '.', $strand, '.', "Name=$gene;product=$prod"
103		];
104		}
105
106		# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
107		# output a sorted GFF3
108
109		sub gff_sort {
110		# sort by seqid, then start pos
111		return ($a->[0] cmp $b->[0]) \|\| ($a->[3] <=> $b->[3]);
112		}
113
114		msg("Found", scalar(@feat), "ribosomal RNA features.");
115		msg("Sorting features and outputting GFF3...");
116		print "##gff-version 3\n";
117		for my $row (sort { gff_sort } @feat) {
118		print join("\t", @$row),"\n";
119		}
120		if ($incseq) {
121		print "##FASTA\n";
122		open FASTA, $fasta;
123		print while (<FASTA>); # `cat $fasta`
124		}
125
126		#----------------------------------------------------------------------
127
128		sub msg {
129		return if $quiet;
130		my $t = localtime;
131		my $line = "[".$t->hms."] @_\n";
132		print STDERR $line;
133		}
134
135		#----------------------------------------------------------------------
136
137		sub err {
138		$quiet=0;
139		msg(@_);
140		exit(2);
141		}
142
143		#----------------------------------------------------------------------
144
145		sub version {
146		print STDERR "$EXE $VERSION\n";
147		exit;
148		}
149
150		#----------------------------------------------------------------------
151
152		sub show_citation {
153		print STDERR << "EOCITE";
154
155		If you use Barrnap in your work, please cite:
156
157		Seemann T (2013)
158		$EXE $VERSION : $DESC
159		$URL
160
161		Thank you.
162
163		EOCITE
164
165		exit;
166		}
167
168		#----------------------------------------------------------------------
169		# Option setting routines
170
171		sub setOptions {
172		use Getopt::Long;
173
174		@Options = (
175		'Options:',
176		{OPT=>"help", VAR=>\&usage, DESC=>"This help"},
177		{OPT=>"version", VAR=>\&version, DESC=>"Print version and exit"},
178		{OPT=>"citation",VAR=>\&show_citation, DESC=>"Print citation for referencing $EXE"},
179		{OPT=>"kingdom=s", VAR=>\$kingdom, DEFAULT=>'bacteria', DESC=>"Kingdom: [b]acteria [a]rchaea"},
180		{OPT=>"quiet!", VAR=>\$quiet, DEFAULT=>0, DESC=>"No screen output"},
181		{OPT=>"threads=i", VAR=>\$threads, DEFAULT=>8, DESC=>"Number of threads/cores/CPUs to use"},
182		{OPT=>"lencutoff=f",VAR=>\$lencutoff, DEFAULT=>0.8, DESC=>"Proportional length threshold to tag as pseudo"},
183		{OPT=>"evalue=f",VAR=>\$evalue, DEFAULT=>1E-6, DESC=>"Similarity e-value cut-off"},
184		{OPT=>"incseq!", VAR=>\$incseq, DEFAULT=>0, DESC=>"Include FASTA input sequences in GFF3 output"},
185		);
186
187		(!@ARGV) && (usage());
188
189		&GetOptions(map {$_->{OPT}, $_->{VAR}} grep { ref } @Options) \|\| usage();
190
191		# Now setup default values.
192		foreach (@Options) {
193		if (ref $_ && defined($_->{DEFAULT}) && !defined(${$_->{VAR}})) {
194		${$_->{VAR}} = $_->{DEFAULT};
195		}
196		}
197		}
198
199		#----------------------------------------------------------------------
200
201		sub usage {
202		print STDERR "Synopsis:\n $EXE $VERSION - $DESC\n";
203		print STDERR "Author:\n $AUTHOR\n";
204		print STDERR "Usage:\n $EXE [options] <chromosomes.fasta>\n";
205		foreach (@Options) {
206		if (ref) {
207		my $def = defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
208		$def = ($def ? ' (default OFF)' : '(default ON)') if $_->{OPT} =~ m/!$/;
209		my $opt = $_->{OPT};
210		$opt =~ s/!$//;
211		$opt =~ s/=s$/ [X]/;
212		$opt =~ s/=i$/ [N]/;
213		$opt =~ s/=f$/ [n.n]/;
214		printf STDERR " --%-15s %s%s\n", $opt, $_->{DESC}, $def;
215		}
216		else {
217		print STDERR "$_\n";
218		}
219		}
220		exit(1);
221		}
222
223		#----------------------------------------------------------------------

+224

-0

bin/barrnap less more

	0	#!/usr/bin/env perl
	1	use strict;
	2	use warnings;
	3	use Time::Piece;
	4	use FindBin;
	5
	6	# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
	7	# global variables
	8
	9	my $EXE = $FindBin::RealScript;
	10	my $VERSION = "0.4-dev";
	11	my $DESC = "Bacterial/Archaeal Ribosomal RNA Predictor";
	12	my $AUTHOR = 'Torsten Seemann <torsten.seemann@monash.edu>';
	13	my $URL = 'http://www.vicbioinformatics.com/';
	14	my $DBDIR = "$FindBin::RealBin/../db";
	15	my $OPSYS = $^O;
	16	my $NHMMER = "$FindBin::RealBin/../binaries/$OPSYS/nhmmer";
	17	my %LENG = ("5S_rRNA"=>119, "16S_rRNA"=>1585, "23S_rRNA"=>3232);
	18
	19	# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
	20	# command line options
	21
	22	my(@Options, $quiet, $kingdom, $threads, $evalue, $lencutoff, $incseq);
	23	setOptions();
	24
	25	# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
	26	# check all is well
	27
	28	msg("This is $EXE $VERSION");
	29	msg("Written by $AUTHOR");
	30	msg("Obtained from $URL");
	31	msg("Detected operating system: $OPSYS");
	32
	33	if (! -x $NHMMER) {
	34	err("No binary for your OS '$OPSYS' is included. If you have one, copy it to $NHMMER.");
	35	}
	36	msg("Using HMMER binary: $NHMMER");
	37
	38	#if (! -r "$DATABASE.h3i") {
	39	# err("The pressed HMM files are missing. Go to the barnapp folder and type 'make database'");
	40	#}
	41	#msg("Found database files: $DATABASE.*");
	42
	43	$threads > 0 or err("Invalid --threads $threads");
	44	msg("Will use $threads threads");
	45
	46	$evalue > 0 or err("Invalid --evalue $evalue");
	47	msg("Setting evalue cutoff to $evalue");
	48
	49	$lencutoff > 0 or err("Invalid --lencutoff $lencutoff");
	50	msg("Will tag genes < $lencutoff x full length as partial genes");
	51
	52	if ($kingdom =~ m/^b/i) {
	53	$kingdom = 'bacteria';
	54	}
	55	elsif ($kingdom =~ m/^a/i) {
	56	$kingdom = 'archaea';
	57	}
	58	else {
	59	err("I don't recognise the --kingdom '$kingdom'. Try 'bacteria' or 'archaea'.");
	60	}
	61
	62	my $hmmdb = "$DBDIR/$kingdom.hmm";
	63	err("Can't find database: $hmmdb") unless -r $hmmdb;
	64	msg("Using database: $hmmdb");
	65
	66	# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
	67	# run the external command
	68
	69	my $fasta = shift @ARGV;
	70	$fasta && -r $fasta or err("Usage: $EXE <file.fasta>");
	71
	72	msg("Running $NHMMER on $fasta ... please wait");
	73	my $cmd = "$NHMMER --cpu $threads -E $evalue --w_length 2000 -o /dev/null --tblout /dev/stdout \Q$hmmdb\E \Q$fasta\E";
	74	my @hits = qx($cmd 2>&1);
	75
	76	# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
	77	# process the output
	78
	79	my @feat;
	80	foreach (@hits) {
	81	chomp;
	82	err("nhmmer failed to run - $_") if m/fail\|error\|core dump\|bus error/i;
	83	next if m/^#/; # comment line
	84	next if m/^\s*$/; # empty line
	85	my @x = split ' ', $_;
	86	err("bad line in nhmmer output - @x") unless defined $x[6] and $x[6] =~ m/^\d+$/;
	87
	88	my($begin,$end,$strand) = $x[6] < $x[7] ? ($x[6],$x[7],'+') : ($x[7],$x[6],'-');
	89	my($seqid, $gene, $prod) = ($x[0], $x[2], $x[2]);
	90
	91	# assumes NAME field in .HMM file is of form "16s_rRNA" etc
	92	$prod =~ s/_r/ ribosomal /; # convert the short ID to an English string
	93
	94	# check for incomplete alignments
	95	my $len = $end-$begin+1;
	96	if ($len < int($lencutoff * $LENG{$gene}) ) {
	97	$prod .= " (partial)";
	98	}
	99
	100	msg("Found:", $gene, $seqid, "L=$len/$LENG{$gene}", "$begin..$end", $strand, $prod);
	101	push @feat, [
	102	$seqid, "$EXE:$VERSION", 'rRNA', $begin, $end, '.', $strand, '.', "Name=$gene;product=$prod"
	103	];
	104	}
	105
	106	# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
	107	# output a sorted GFF3
	108
	109	sub gff_sort {
	110	# sort by seqid, then start pos
	111	return ($a->[0] cmp $b->[0]) \|\| ($a->[3] <=> $b->[3]);
	112	}
	113
	114	msg("Found", scalar(@feat), "ribosomal RNA features.");
	115	msg("Sorting features and outputting GFF3...");
	116	print "##gff-version 3\n";
	117	for my $row (sort { gff_sort } @feat) {
	118	print join("\t", @$row),"\n";
	119	}
	120	if ($incseq) {
	121	print "##FASTA\n";
	122	open FASTA, $fasta;
	123	print while (<FASTA>); # `cat $fasta`
	124	}
	125
	126	#----------------------------------------------------------------------
	127
	128	sub msg {
	129	return if $quiet;
	130	my $t = localtime;
	131	my $line = "[".$t->hms."] @_\n";
	132	print STDERR $line;
	133	}
	134
	135	#----------------------------------------------------------------------
	136
	137	sub err {
	138	$quiet=0;
	139	msg(@_);
	140	exit(2);
	141	}
	142
	143	#----------------------------------------------------------------------
	144
	145	sub version {
	146	print STDERR "$EXE $VERSION\n";
	147	exit;
	148	}
	149
	150	#----------------------------------------------------------------------
	151
	152	sub show_citation {
	153	print STDERR << "EOCITE";
	154
	155	If you use Barrnap in your work, please cite:
	156
	157	Seemann T (2013)
	158	$EXE $VERSION : $DESC
	159	$URL
	160
	161	Thank you.
	162
	163	EOCITE
	164
	165	exit;
	166	}
	167
	168	#----------------------------------------------------------------------
	169	# Option setting routines
	170
	171	sub setOptions {
	172	use Getopt::Long;
	173
	174	@Options = (
	175	'Options:',
	176	{OPT=>"help", VAR=>\&usage, DESC=>"This help"},
	177	{OPT=>"version", VAR=>\&version, DESC=>"Print version and exit"},
	178	{OPT=>"citation",VAR=>\&show_citation, DESC=>"Print citation for referencing $EXE"},
	179	{OPT=>"kingdom=s", VAR=>\$kingdom, DEFAULT=>'bacteria', DESC=>"Kingdom: [b]acteria [a]rchaea"},
	180	{OPT=>"quiet!", VAR=>\$quiet, DEFAULT=>0, DESC=>"No screen output"},
	181	{OPT=>"threads=i", VAR=>\$threads, DEFAULT=>8, DESC=>"Number of threads/cores/CPUs to use"},
	182	{OPT=>"lencutoff=f",VAR=>\$lencutoff, DEFAULT=>0.8, DESC=>"Proportional length threshold to tag as pseudo"},
	183	{OPT=>"evalue=f",VAR=>\$evalue, DEFAULT=>1E-6, DESC=>"Similarity e-value cut-off"},
	184	{OPT=>"incseq!", VAR=>\$incseq, DEFAULT=>0, DESC=>"Include FASTA input sequences in GFF3 output"},
	185	);
	186
	187	(!@ARGV) && (usage());
	188
	189	&GetOptions(map {$_->{OPT}, $_->{VAR}} grep { ref } @Options) \|\| usage();
	190
	191	# Now setup default values.
	192	foreach (@Options) {
	193	if (ref $_ && defined($_->{DEFAULT}) && !defined(${$_->{VAR}})) {
	194	${$_->{VAR}} = $_->{DEFAULT};
	195	}
	196	}
	197	}
	198
	199	#----------------------------------------------------------------------
	200
	201	sub usage {
	202	print STDERR "Synopsis:\n $EXE $VERSION - $DESC\n";
	203	print STDERR "Author:\n $AUTHOR\n";
	204	print STDERR "Usage:\n $EXE [options] <chromosomes.fasta>\n";
	205	foreach (@Options) {
	206	if (ref) {
	207	my $def = defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
	208	$def = ($def ? ' (default OFF)' : '(default ON)') if $_->{OPT} =~ m/!$/;
	209	my $opt = $_->{OPT};
	210	$opt =~ s/!$//;
	211	$opt =~ s/=s$/ [X]/;
	212	$opt =~ s/=i$/ [N]/;
	213	$opt =~ s/=f$/ [n.n]/;
	214	printf STDERR " --%-15s %s%s\n", $opt, $_->{DESC}, $def;
	215	}
	216	else {
	217	print STDERR "$_\n";
	218	}
	219	}
	220	exit(1);
	221	}
	222
	223	#----------------------------------------------------------------------

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