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Changeset 262

Timestamp:

09/15/09 13:26:04 (2 months ago)

Author:

cholt

Message:

fix maker2jbrowse

Files:

bin/maker2jbrowse (modified) (5 diffs)

Legend:

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: Added
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bin/maker2jbrowse

r261	r262
84	84	}
85	85
86		if(@files){
	86	if(!@files){
87	87	print $usage;
88	88	exit();
…	…
109	109
110	110	#MAKER anotations
111		$commans{gene} = ' --tracklabel "Genes" --key "Genes" --getType --getLabel --autocomplete label --cssclass feature5 --type gene';
112		$comman~~s{mRNA}~~ = ' --tracklabel "Transcripts" --key "Transcripts" --getType --getSubs --getLabel --autocomplete label --cssclass transcript --subfeatureClasses \'{"exon": "transcript-exon", "CDS": "transcript-CDS", "UTR": "transcript-UTR"}\' --arrowheadClass transcript-arrowhead --type mRNA';
	111	$commands{gene} = ' --tracklabel "Genes" --key "Genes" --getType --getLabel --autocomplete label --cssclass feature5 --type gene';
	112	$commands{maker} = ' --tracklabel "Transcripts" --key "Transcripts" --getType --getSubs --getLabel --autocomplete label --cssclass transcript --subfeatureClasses \'{"exon": "transcript-exon", "CDS": "transcript-CDS", "UTR": "transcript-UTR"}\' --arrowheadClass transcript-arrowhead --type mRNA';
113	113
114	114	#ab initio gene predictions
115		$commans{snap} = ' --tracklabel "SNAP" --key "SNAP" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-CDS"}\' --arrowheadClass transcript-arrowhead --type match:snap';
116		$commans{augustus} = ' --tracklabel "Augustus" --key "Augustus" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-CDS"}\' --arrowheadClass transcript-arrowhead --type match:augustus';
117		$commans{genemark} = ' --tracklabel "GeneMark" --key "GeneMark" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-CDS"}\' --arrowheadClass transcript-arrowhead --type match:genemark';
118		$commans{fgenesh} = ' --tracklabel "FGENESH" --key "FGENESH" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-CDS"}\' --arrowheadClass transcript-arrowhead --type match:fgenesh';
	115	$commands{snap} = ' --tracklabel "SNAP" --key "SNAP" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-CDS"}\' --arrowheadClass transcript-arrowhead --type match:snap';
	116	$commands{snap_masked} = ' --tracklabel "SNAP" --key "SNAP" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-CDS"}\' --arrowheadClass transcript-arrowhead --type match:snap_masked';
	117	$commands{augustus} = ' --tracklabel "Augustus" --key "Augustus" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-CDS"}\' --arrowheadClass transcript-arrowhead --type match:augustus';
	118	$commands{augustus_masked} = ' --tracklabel "Augustus" --key "Augustus" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-CDS"}\' --arrowheadClass transcript-arrowhead --type match:augustus_masked';
	119	$commands{genemark} = ' --tracklabel "GeneMark" --key "GeneMark" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-CDS"}\' --arrowheadClass transcript-arrowhead --type match:genemark';
	120	$commands{genemark_masked} = ' --tracklabel "GeneMark" --key "GeneMark" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-CDS"}\' --arrowheadClass transcript-arrowhead --type match:genemark_masked';
	121	$commands{fgenesh} = ' --tracklabel "FGENESH" --key "FGENESH" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-CDS"}\' --arrowheadClass transcript-arrowhead --type match:fgenesh';
	122	$commands{fgenesh_masked} = ' --tracklabel "FGENESH" --key "FGENESH" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-CDS"}\' --arrowheadClass transcript-arrowhead --type match:fgenesh_masked';
119	123
120	124	#evidence alignments
121		$commans{blastx} = ' --tracklabel "BLASTX" --key "BLASTX" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type protein_match:blastx';
122		$comman~~s{blastn} = ' --tracklabel "BLASTN" --key "BLASTN" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type protein~~_match:blastn';
123		$comman~~s{tblastx} = ' --tracklabel "TBLASTX" --key "TBLASTX" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type protein~~_match:tblastx';
124		$comman~~s{est2genome} = ' --tracklabel "est2genome" --key "est2genome" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type protein~~_match:est2genome';
125		$commans{protein2genome} = ' --tracklabel "protein2genome" --key "protein2genome" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type protein_match:protein2genome';
	125	$commands{blastx} = ' --tracklabel "BLASTX" --key "BLASTX" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type protein_match:blastx';
	126	$commands{blastn} = ' --tracklabel "BLASTN" --key "BLASTN" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type expressed_sequence_match:blastn';
	127	$commands{tblastx} = ' --tracklabel "TBLASTX" --key "TBLASTX" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type expressed_sequence_match:tblastx';
	128	$commands{est2genome} = ' --tracklabel "est2genome" --key "est2genome" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type expressed_sequence_match:est2genome';
	129	$commands{protein2genome} = ' --tracklabel "protein2genome" --key "protein2genome" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type protein_match:protein2genome';
126	130
127	131	#repeats
128		$comman~~s{repeatmasker} = ' --tracklabel "RepeatMasker" --key "RepeatMasker" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type protein_~~match:repeatmasker';
129		$comman~~s{repeaqtrunner~~} = ' --tracklabel "RepeatRunner" --key "RepeatRunner" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type protein_match:blastx:repeatmask';
	132	$commands{repeatmasker} = ' --tracklabel "RepeatMasker" --key "RepeatMasker" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type match:repeatmasker';
	133	$commands{blastx:repeatmask} = ' --tracklabel "RepeatRunner" --key "RepeatRunner" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type protein_match:blastx:repeatmask';
130	134
131	135
…	…
133	137	my $gff;
134	138	my $fasta;
	139	my %tracks;
135	140
136	141	open(IN, "< $file");
…	…
146	151	}
147	152	else{
	153	if($line !~ /^\#/ && $line =~ /[^\t]\t([^\t])\t/){
	154	$val = $1;
	155	$tracks{$1}++;
	156	$tracks{gene}++ if($1 eq 'maker'); #add gene locus track
	157	}
	158
148	159	$gff .= $line;
149	160	next;
…	…
169	180	close($fh);
170	181
171		while(my $track = each %~~command~~s){
	182	while(my $track = each %tracks){
172	183	my $command = $JB;
	184
	185	die "ERROR: No track information for source \'$track\'\n\n";
	186
173	187	$command .= $commands{$track};
174	188	$command .= " --gff $fname";

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