class BlastTypeParser
Public Class Methods
new(contig_type,hit_type,file,all=FALSE)
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# File lib/gene_assembler/blast_type_parser.rb, line 5 def initialize(contig_type,hit_type,file,all=FALSE) @file=file @dataset=create_dataset @all=all data=parse_file(file) load_dataset(data,contig_type,hit_type) end
Public Instance Methods
load_dataset(data,contig_type,hit_type)
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# File lib/gene_assembler/blast_type_parser.rb, line 13 def load_dataset(data,contig_type,hit_type) # Introduce datos del blast en clases contig/hit/hsp data.querys.each do |item| if item.hits.empty? #Descartamos querys q no hayan dado nigun match next end contig=@dataset.add_contig(item.query_def) #query_def -> nombre de la query (nuestro contig) contig.length=item.full_query_length #full_query_length -> longitud de la query contig.type=contig_type populate_extra_atributes(contig,item) last_hit_name='' hit='' item.hits.each do |ht| #Clasificacion hits del blast en hits-hsps if ht.subject_id != last_hit_name #Hit hit=contig.add_hit(ht.subject_id, ht.full_subject_length, ht.q_frame, hit_type) end hsp=hit.add_hsp(ht.q_beg+1, ht.q_end+1, ht.s_beg+1, ht.s_end+1, ht.align_len, ht.score, ht.ident, ht.gaps) # +1 xq gema parser blast resta 1 a todo hsp.type='match_part' last_hit_name=ht.subject_id end contig.hits_sort! end end
populate_extra_atributes(contig,item)
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# File lib/gene_assembler/blast_type_parser.rb, line 37 def populate_extra_atributes(contig,item) end