Module: Exodb::Utils

Defined in:
lib/exodb/utils.rb,
lib/exodb/rositza.rb,
lib/exodb/rositza/load.rb,
lib/exodb/utils/upload_var.rb,
lib/exodb/utils/upload_generef.rb

Class Method Summary collapse

Class Method Details

.guess_miriam(str) ⇒ String

Guess the type of id

Parameters:

Returns:

  • (String) —

    a miriam registry or the string itself incase cannot guess



30
31
32
33
34
35
36
37
38
39
40
41
42
43
 
# File 'lib/exodb/utils.rb', line 30

def guess_miriam(str)
	case str
	when /\A((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+|(NZ\_[A-Z]{4}\d+))(\.\d+)?\z/
		return "urn:miriam:refseq:#{str}"
	when /\A((ENS[A-Z]*[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))\z/
		return "urn:miriam:ensembl:#{str}"
	when /\A((HGNC|hgnc):)?\d{1,5}\z/
		return "urn:miriam:hgnc:#{str}"
	when /\ACCDS\d+\.\d+\z/
		return "urn:miriam:ccds:#{str}"
	else
		return str
	end
end

.load_indel_from_merge(mergefile) ⇒ Object 



65
66
67
68
69
70
71
72
73
74
75
76
 
# File 'lib/exodb/rositza/load.rb', line 65

def load_indel_from_merge(mergefile)
	
	File.open(mergefile).each do |line|
		record = line.chomp.split("\t")
		p record[0..21]
		#others = record[22..-1]
		#until others.empty?
		#	p others.shift(11)
		#end
	end
	
end

.load_sample_from_csv(csvfile) ⇒ Object 



38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
 
# File 'lib/exodb/rositza/load.rb', line 38

def load_sample_from_csv(csvfile)
	CSV.read(csvfile, col_sep: "\t", headers: true).each do |record|
		
		sample = Tumor.new({oid: record["SampleFinal"],
						type: record["Type"].downcase,
						typeid: "urn:miriam:bioportal.meddra:#{record["Type"] =~ /^spitz /i ? '10041632' : record["Type"] =~ /^spitzoid /i ? '10072450' : '10028679'}",
						patient: record["SampleFinal"].split('T')[0],
						preferred: record["Preferred"] == 'Y' ? true : false,
						paired: record["merge41final"] =~ /\Apaired\z/i ? true : false},
						labels: {})
		
		sample.add_to_dataset('internal.ds:000001')
		
		p sample.save!
		
	end
end

.load_variant_from_ann(annfile) ⇒ Object 



56
57
58
59
60
61
62
63
 
# File 'lib/exodb/rositza/load.rb', line 56

def load_variant_from_ann(annfile)
	
	File.open(annfile).each do |line|
		record = line.chomp.split("\t")
		p record
	end
	
end

.load_variant_from_csv(csvfile) ⇒ Object 



20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
 
# File 'lib/exodb/rositza/load.rb', line 20

def load_variant_from_csv(csvfile)
	
	CSV.read(csvfile, col_sep: "\t", headers: true).each do |record|
		
		var = SNV.new()
		var.parse_location("#{record["chromosome"]}:#{record["start position"]}")
		var.reference = record["ref nucleotide"].split('/')[0]
		var.alternate = record["var nucleotide"].split('/').uniq
		var.somaticStatus = record["Somatic Status"]
		var.reads = record["Reads"]
		var.predicted_damage = record["PolyPhen"] =~ /probably_damaging/ || record["SIFT"] =~ /deleterious/i || record["PROVEAN"] =~ /deleterious/i ? true : false
		var.aachange = record["AA Change"]
		var.add_to_sample(record["cell"])
		
		p var.save!
	end
end

.load_variant_from_merge(mergefile) ⇒ Object 



78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
 
# File 'lib/exodb/rositza/load.rb', line 78

def load_variant_from_merge(mergefile)
	
	File.open(mergefile).each do |line|
		record = line.chomp.split("\t")
		
		header = record[0..15]
		
		list = record[16..-1]
		
		until list.empty?
			
			sampledata = list.shift(7)
			snvq = Exodb::Variant.where(oid: "#{header[2]}:#{header[3]}:#{sampledata[0]}")
			if snvq.exists?
				snv = snvq.first
				snv.temp.push(header[0..6].join("\t"))
				p snv.save!
			else
				snv = Exodb::Variant.new()
				snv.parse_location("#{header[2]}:#{header[3]}..#{header[3]}")
				snv.reference = header[10]
				snv.pileupt = sampledata[6]
				snv.temp = [] if snv.temp == nil
				snv.temp.push(header[0..6].join("\t"))
				snv.add_to_sample(sampledata[0])
				p snv.save!
			end
		end
	end
	
end

.upload_generef_from_gff3(filename, assembly = nil) ⇒ Object

Upload gene information to database using gff3 and genome sequence fasta file

Parameters:

  • gff3 (String) —

    file

  • assembly (String) (defaults to: nil) —

    name [default: gff file name]



23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
 
# File 'lib/exodb/utils/upload_generef.rb', line 23

def upload_generef_from_gff3(filename, assembly = nil)
	
	gff = Bio::GFF::GFF3.new(File.open(filename).read)
	
	processDbxref = lambda do |str|
		case str
		when /^GeneID/
			return "urn:miriam:ncbigene:#{str.split(/:/)[1]}"
		when /^HGNC/
			return "urn:miriam:hgnc:#{str}"
		when /^HPRD/
			return "urn:miriam:hprd:#{str.split(/:/)[1]}"
		when /^miRBase/
			return "urn:miriam:mirbase:#{str.split(/:/)[1]}"
		when /^Genbank/
			return "urn:miriam:refseq:#{str.split(/:/)[1]}"
		when /^CCDS/
			return "urn:miriam:ccds:#{str.split(/:/)[1]}"
		when /^MIM/
			return "urn:miriam:omim:#{str.split(/:/)[1]}"
		else
			return str
		end
	end
	
	assembly = assembly ? assembly : File.basename(filename, '.gff3')
	
	regions = {}
	genes = {}
	seq = {}
	
	
	gff.records.each do |e|
		
		case e.feature
		when 'region'
			e.attributes.each do |attr|
				case attr[0]
				when 'chromosome'
					regions[e.seqname] = attr[1] == 'X' ? 23 : attr[1] == 'Y' ? 24 : attr[1].to_i
				end
			end
			
			if File.exist?("./genome/#{e.seqname}.fa")
				seq = {}
				Bio::FlatFile.open(Bio::FastaFormat, "./genome/#{e.seqname}.fa").each {|fasta| seq[fasta.acc_version] = fasta.to_seq}
			end
			
		when 'gene', 'tRNA'
			
			gene = {type: 'gene', xrefs: [], strand: e.strand, chrrefseq: "#{guess_miriam(e.seqname)}", location: "#{e.seqname =~ /\ANC_/ ? regions[e.seqname] : e.seqname}:#{e.start}..#{e.end}", childs: [], exon: [], cds: []}
			
			e.attributes.each do |attr|
				case attr[0]
				when 'Dbxref'
					gene[:xrefs].push(processDbxref.call(attr[1]))
				when 'Name'
					gene[:xrefs].push("urn:miriam:hgnc.symbol:#{attr[1]}") if attr[1] !~ /^LOC\d+$/
				when 'pseudo'
					gene[:psuedo] = attr[1] == 'true' ? true : false
				when 'ID'
					gene[:id] = attr[1]
				end
			end
			
			gene[:sequence] = seq[e.seqname].subseq(e.start.to_i, e.end.to_i).to_s if seq.has_key?(e.seqname)
			gene[:oid] = gene[:location]
			genes[gene[:id]] = gene
			
		when /\A(transcript|[^t]*RNA)/
			rna = {type: 'rna', xrefs: [], strand: e.strand, chr: regions[e.seqname], location: "#{regions[e.seqname]}:#{e.start}..#{e.end}", exon: [], cds: []}
			
			e.attributes.each do |attr|
				case attr[0]
				when 'Dbxref'
					rna[:xrefs].push(processDbxref.call(attr[1]))
				when 'pseudo'
					rna[:psuedo] = attr[1] == 'true' ? true : false
				when 'ID'
					rna[:id] = attr[1]
				when 'Parent'
					rna[:parent] = attr[1]
				end
			end
			
			genes[rna[:id]] = rna
			genes[rna[:parent]][:childs].push(rna[:id]) if rna[:parent]
			
		when 'exon'
			e.attributes.each do |attr|
				case attr[0]
				when 'Parent'
					genes[attr[1]][:exon].push([e.start, e.end].sort)
				end
			end
		when 'CDS'
			e.attributes.each do |attr|
				case attr[0]
				when 'Parent'
					genes[attr[1]][:cds].push([e.start, e.end].sort)
				end
			end
		end
	end
	
	genes.each_pair do |k, v|
		if v[:type] == 'gene'
			
			gene = Generef.new()
			gene.oid = v[:oid] if v.has_key?(:oid)
			gene.xrefs = v[:xrefs]
			gene.parse_location(v[:location])
			gene.chrrefseq = v[:chrrefseq]
			gene.strand = v[:strand]
			gene.psuedo = v[:psuedo] if v[:psuedo]
			gene.genomeref = assembly
			gene.sequence = v[:sequence] if v.has_key?(:sequence)
			
			v[:childs].each do |child|
				
				rna = Isoform.new()
				data = genes[child]
				rna.xrefs = data[:xrefs]
				rna.exon = data[:exon].sort
				rna.cds = data[:cds].sort
				
				gene.isoforms.push(rna)
				
			end
			
			puts "STATUS: #{gene.save! ? "SUCCESS" : "FAIL"}: Deposit Gene reference #{gene.xrefs[0]}"
			
		end
		
	end
	
	
end