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Changeset 263

Timestamp:

09/15/09 16:29:51 (2 months ago)

Author:

cholt

Message:

include JBrowse configuration files

Files:

Legend:

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bin/maker2jbrowse

r262	r263
40	40
41	41	This script takes MAKER produced GFF3 files and dumps them into a
42		JBrowse for you using a pre-configured JSON tracks.
	42	JBrowse for you using pre-configured JSON tracks.
43	43
44	44	OPTIONS:
…	…
55	55	);
56	56
57		~~my $dbname = shift;~~
58	57	my @files;
59	58
…	…
113	112
114	113	#ab initio gene predictions
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';
	114	$commands{snap} = ' --tracklabel "SNAP" --key "SNAP" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-exon2"}\' --arrowheadClass transcript-arrowhead --type match:snap';
	115	$commands{snap_masked} = ' --tracklabel "SNAP" --key "SNAP" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-exon2"}\' --arrowheadClass transcript-arrowhead --type match:snap_masked';
	116	$commands{augustus} = ' --tracklabel "Augustus" --key "Augustus" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-exon3"}\' --arrowheadClass transcript-arrowhead --type match:augustus';
	117	$commands{augustus_masked} = ' --tracklabel "Augustus" --key "Augustus" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-exon3"}\' --arrowheadClass transcript-arrowhead --type match:augustus_masked';
	118	$commands{genemark} = ' --tracklabel "GeneMark" --key "GeneMark" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-exon4"}\' --arrowheadClass transcript-arrowhead --type match:genemark';
	119	$commands{genemark_masked} = ' --tracklabel "GeneMark" --key "GeneMark" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-exon4"}\' --arrowheadClass transcript-arrowhead --type match:genemark_masked';
	120	$commands{fgenesh} = ' --tracklabel "FGENESH" --key "FGENESH" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-exon5"}\' --arrowheadClass transcript-arrowhead --type match:fgenesh';
	121	$commands{fgenesh_masked} = ' --tracklabel "FGENESH" --key "FGENESH" --getType --getSubs --getLabel --cssclass transcript --subfeatureClasses \'{"match_part": "transcript-exon5"}\' --arrowheadClass transcript-arrowhead --type match:fgenesh_masked';
123	122
124	123	#evidence alignments
125		$commands{blast~~x} = ' --tracklabel "BLASTX" --key "BLASTX" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part"}\' --type protein_match:blastx~~';
126		$commands{blast~~n} = ' --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';
	124	$commands{blastn} = ' --tracklabel "BLASTN" --key "BLASTN" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part4"}\' --type expressed_sequence_match:blastn';
	125	$commands{blastx} = ' --tracklabel "BLASTX" --key "BLASTX" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part5"}\' --type protein_match:blastx';
	126	$commands{tblastx} = ' --tracklabel "TBLASTX" --key "TBLASTX" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part6"}\' --type expressed_sequence_match:tblastx';
	127	$commands{est2genome} = ' --tracklabel "est2genome" --key "est2genome" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part3"}\' --type expressed_sequence_match:est2genome';
	128	$commands{protein2genome} = ' --tracklabel "protein2genome" --key "protein2genome" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part2"}\' --type protein_match:protein2genome';
130	129
131	130	#repeats
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';
	131	$commands{repeatmasker} = ' --tracklabel "RepeatMasker" --key "RepeatMasker" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part7"}\' --type match:repeatmasker';
	132	$commands{'blastx:repeatmask'} = ' --tracklabel "RepeatRunner" --key "RepeatRunner" --getType --getSubs --cssclass generic_parent --subfeatureClasses \'{"match_part": "match_part7"}\' --type protein_match:blastx:repeatmask';
134	133
135	134
…	…
150	149	next;
151	150	}
	151	elsif($line =~ /[^\t]\t[^\t]\tcontig\t/){
	152	next; #skip contig line
	153	}
152	154	else{
153	155	if($line !~ /^\#/ && $line =~ /[^\t]\t([^\t])\t/){
154		~~$val = $1;~~
155	156	$tracks{$1}++;
156	157	$tracks{gene}++ if($1 eq 'maker'); #add gene locus track
…	…
183	184	my $command = $JB;
184	185
185		die "ERROR: No track information for source \'$track\'\n\n";
	186	die "ERROR: No track information for source \'$track\'\n\n" if(! exists $commands{$track});
186	187
187	188	$command .= $commands{$track};

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Changeset 263

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bin/maker2jbrowse

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